Varroa-virus meta-transcriptomic analysis
Nurit Eliash and Sasha Mikheyev
1/22/2020
In this study we investigated virus-virus and vector-virus interactions by combining two approaches:
- meta-transciptomic analysis, and
- gene-silencing experiments.
In the following code pipeline we present the (1) meta-transcriptomic analysis.
Here we looked at the overall viral landscape in the different libraries, detected vector modules (co-expressing genes using gene-network analysis), and correlated the viruses’ abundance to the vector modules. Last, we tested if the virus abundance matrix can predict the virus-vector interaction.
In this R markdown document we present the meta-transcriptomic analysis step by step in a way that can be reproduced using the input files available on the GitHub web-page. The following chunks are ordered as the sections in the Materials and Methods of the manuscript “Diverse and rapidly evolving viral strategies modulate arthropod vector gene expression”, Eliash et al. (2022). All of the referred tables and figures can be found in the manuscript as well.
RNAseq data collection, mapping and filtration
Sequence Read Archive (SRA) data collection
We searched for the term “varroa” in the SRA databases (NCBI, January 2020) with the following filters:
- Source: “RNA”
- Library Strategy: “RNA-seq” (Random sequencing of whole transcriptome)
- Library Source: “TRANSCRIPTOMIC”, “VIRAL RNA”
- We included only whole mites (partial organs not included)
Reads mapping and transcripts quantification
The reads were mapped to both available varroa genome (Vdes_3.0, accession number: GCF_002443255, (Tehcer et al. 2019)), and to the genomes of 23 selected viruses (table 1). The alignment and estimation of transcript and virus abundances were done using Kallisto (Bray et al. 2016) (version 0.46.1 with default options). The abundances were outputted in transcripts per million (TPM) units.
Load data and RNAseq library filtration
Load libraries
library("dplyr")
library("tidyverse")
library("vegan")
library("DESeq2")
library("ggfortify")
library("WGCNA")
options(stringsAsFactors = FALSE) # Allow multi-threading within WGCNA. This helps speed up certain calculations.
library("rmarkdown")
library("knitr") # for the markdown
library("kableExtra") # for creating a scrolling table
library("ggplot2") # for plotting
library("ape") # for mantel.test
library("Biostrings")
library("ggrepel") # for spreading text labels on the plot
library("scales") # for axis labels notation
library("GO.db") # for GO term annotation
library("reshape2")
library("RSQLite")
library("AnnotationDbi") # for GO term annotation
library("GSEABase")
library("GOstats")
library("maps") # for the map background
library("htmltools")
library("rgdal")
library("grid")
library("gridExtra")
library("GeneOverlap") # for making the overlapping genes
library("cluster")
library("rmdformats")
library("corrplot") # for virus-virus correlation
library("viridis")
library("hrbrthemes")
library("ggthemes")
library("RColorBrewer")
library("naniar")
library("kableExtra")
knitr::opts_chunk$set(echo = TRUE)
setwd("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks") #set the directory as the local GitHub local repositoryCreate the initial input data frame
The mapped libraries were used to create the initial data frame, in which each column is a SRR library, and each row is an isoform. The cells contain the isoform TPM.
The output data frame contains 35,669 isoforms of the selected 71 varroa libraries. The first 35,641 rows are varroa genes, and the last 28 rows are reads that matched to the selected viruses (for viruses’ details, see Table 1).
# First make a function for making the mapped reads (output of kallisto) into a data frame
read_kallisto <- function(filename) {
sampleName <- sub("data/kallisto/(.*).tsv.gz","\\1", filename)
return(read_tsv(filename) %>%
dplyr::select(!!sampleName := tpm))
}
# now make the data frame, which contain all 71 libraries:
df_71 <- list.files(path = "data/kallisto", full.names = TRUE) %>%
lapply(read_kallisto) %>%
bind_cols()
# add a column "target_id" with the isoform/virus ID
df_71$target_id <- list.files(path = "data/kallisto", full.names = TRUE)[1] %>%
read_tsv() %>%
dplyr::select(target_id) %>%
pull()
#save(df_71, file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/data/kallisto_71.rds")Join varroa isoforms into genes
# Next, we join isoforms that belong to the same gene.
# Load the data frame created in the former chunk
load(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/data/kallisto_71.rds")
# Import the varroa transcripts ("target_id") and their corresponding gene ("gene_id").
varroa_isoforms <- read_tsv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/data/gene2isoform.txt.gz", col_names = c("gene_id", "target_id"))
# Join the varroa transcripts (varroa_isoforms), and the library tpm (df), by the isoform ID ("target_id"). As we do "left_join", the final data frame of "gene_tpm" contain ONLY varroa genes, excluding viruses' tpm.
gene_tpm_71 <- left_join(varroa_isoforms, df_71, by = "target_id")
# Collapse isoforms ("target_id") to a single row of a gene ("gene_id"), and sum the tpm(s) per gene per library
gene_tpm_collps_71 <- gene_tpm_71 %>%
gather("library","tpm", -target_id, -gene_id) %>%
group_by(gene_id, library) %>%
summarise(gene_tpm_71 = sum(tpm))
# spread the table again, by library
final_gene_tpm_71 <- spread(gene_tpm_collps_71, key = "library", value = "gene_tpm_71") %>% column_to_rownames('gene_id')
# this table will be used for all further analyses
# save(final_gene_tpm_71, file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/final_gene_tpm_71.rds")Next, we perform Principle Component Analysis (PCA) on varroa genes, to detect outlierd libraries
Detect outlier libraries based on PCA (Figure S2)
# load the table
load(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/final_gene_tpm_71.rds")
# Before PCA, we transpose the table "final_gene_tpm_71", and transform (log10+0.000001)
final_gene_tpm_71_T<- transposeBigData(log10(final_gene_tpm_71 + 0.000001))
PCA_71 <- prcomp(final_gene_tpm_71_T)
p71 <- autoplot(PCA_71, label = TRUE, x = 1, y = 2)+
ggtitle("a. PCA of 71 libraries based on gene expression")
# Five libraries are obvious outliers: "SRR5109825", "SRR5109827", "SRR533974" , "SRR3927496", "SRR8867385".
final_gene_tpm_66_T <- final_gene_tpm_71_T %>%
rownames_to_column("library") %>%
dplyr::filter(!(library %in% c("SRR5109825", "SRR5109827", "SRR533974" , "SRR3927496", "SRR8867385"))) %>% column_to_rownames("library")
PCA_66 <- prcomp(final_gene_tpm_66_T)
p66 <- autoplot(PCA_66, label = TRUE, x = 1, y = 2)+
ggtitle("b. PCA of 66 libraries based on gene expression")# plot the two PCA plots side by side:
par(mar = c(4, 4, .1, .1))
p71
p66
# when we remove them and repeat the PCA (Fig S2b), the library scatter more homogeneously.
Figure S1. PCA of varroa SRA libraires based on their genes TPM. a. All 71 libraries. The outlier libraries can be seen on the left side of the plot. These 5 libraries were excluded from further analysis. b. the final 66 libraries used for the analysis.
After filtering outlier libraries (based on PCA analysis), we used the left 66 SRAs belonging to 9 studies of varroa RNAseq for further analyses (details of the final libraries available in Table S5).
Remove outlier libraries and save data frame of varroa genes for later WGCNA
# We remove the five outlier libraries from the data frame, and save for subsequent analyses
load(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/data/kallisto_71.rds")
df <- df_71 %>% dplyr::select(-c("SRR5109825", "SRR5109827", "SRR533974" , "SRR3927496", "SRR8867385"))
# In addition, we save the final varroa genes TPM values per library, of the filtered 66 libraries, for the Gene Network analysis.
for_modules <- final_gene_tpm_71 %>%
dplyr::select(-c("SRR5109825", "SRR5109827", "SRR533974" , "SRR3927496", "SRR8867385")) %>%
transposeBigData()
#save(for_modules, file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/for_modules.rds")Viral abundance analysis
AIM: describing viruses’ abundance in the different varroa SRA libraries.
We first prepare the suitable data frame containing viruses’ load in each library, by joining the initial df, with viruses’ IDs:
# read the viruses IDs:
virusId <- read_tsv("data/viruses.txt", col_names = c("target_id", "description"))
# Varroa orthomyxovirus-1 (VOV-1) virus genome has been described in 6 different segments (Levin et al. 2016). Before proceeding for viral abundance analysis we sum all VOV-1 segments into one.
virusId[3:8, 2] <- "VOV_1"
x <- left_join(virusId, df, by = "target_id") %>% dplyr::select(-target_id)
# Sum all 6 segments TPM in each library in a separate table 'VOV_1':
VOV_1 <- x %>%
dplyr::slice(3:8) %>%
group_by(description) %>%
summarize_all(sum)
#filter out the segments of VOV_1,
x <- dplyr::filter(x, description != "VOV_1")
# insert VOV_1 in row 3
r <- 3
insertRow <- function(x, VOV_1, r) {
x[seq(r+1,nrow(x)+1),] <- x[seq(r,nrow(x)),]
x[r,] <- VOV_1
x
}
viruses_load <- insertRow(x, VOV_1, r)
head(viruses_load)
# save the viral load data frame
#save(viruses_load, file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/viruses_load.rds")Figure 1. Vizualize viruses distribution and abundance in a heat-map
# (3) heat-map of viruses loads (log10(tpm)) per library
# load the former virus data
load(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/viruses_load.rds")
# plot the viruses abundance in each library
# make a vector of the new viruses order
new_order <- c("DWVa", "VDV1/DWVb", "VDV2", "BMV","VOV_1","ARV_2", "DWVc", "AmFV", "VDV3", "ABPV", "VTLV", "SV", "BQCV","VDV4", "IAPV", "KBV", "SBPV", "LSV","CBPV" ,"AFV", "ANV", "VPVL_46","VPVL_36")
# re-order the viruses, based on viral load and viral abundance (from highest, on the left, to lowest on the right), and change the names of the viruses to match their common name in the literature:
viruses_load_arranged <- viruses_load %>%
mutate(description = factor(description, levels = new_order)) %>%
arrange(description) %>%
mutate(across("description", str_replace, "VOV_1", "VOV-1")) %>%
mutate(across("description", str_replace, "ARV_2", "ARV-2")) %>%
mutate(across("description", str_replace, "SV", "SBV")) %>%
mutate(across("description", str_replace, "LSBV", "LSV")) %>%
mutate(across("description", str_replace, "VDV1/DWVb", "DWVb"))
# lock in factor level order
viruses_load_arranged$description <- factor(viruses_load_arranged$description, levels = viruses_load_arranged$description)
# spread the df
virus_abund <- viruses_load_arranged %>%
gather("library", "tpm", -description)
virus_abund[, 3] <- (virus_abund[,3]+ 0.000001) # I added 0.000001 to each value, so there will be no zeros
virus_abund[, 3] <- log10(virus_abund[,3]) # tpm in log10 scale
virus_abund <- replace_with_na(virus_abund, replace = list(tpm = -6)) # whenever there is a zero value (-6), I replace with NA, so the cell will appear in gray color.
# now make a heat map
ggplot(data = virus_abund, mapping = aes(x = description,
y = library,
fill = tpm)) +
scale_fill_gradient2(low="#FFFFCC", mid = "#FF9933", high="#990000", na.value = "grey92") +
geom_tile() +
theme_linedraw() +
xlab(label = "Viruses") +
ylab(label = "Varroa SRA libraries") +
labs(fill = "Viral load \n log10(TPM)") +
theme(axis.text.x = element_text(angle = 45, hjust = 1, size = 15)) +
theme(axis.text.y = element_text(size = 12)) +
theme(axis.ticks = element_blank()) +
theme(axis.title = element_text(size = 20))
Figure 1. Viral load is diverse across the different varroa libraries. Values are log10 transformed of the reads’ TPM (transcript per millions). Zero values are marked in grey (i.e., none of the reads in this library mapped to this virus). The viruses’ names are abbreviated as described in Table 1. More information on the viruses’, accession numbers, genome length, references and etc. are available in supp table S1. Members of the Iflavirus family are the most prevalent, yet while some viruses are homogenous across libraries (VDV2), others are highly diverse (e.g. DWVa and DWVb).
Figure 2a. Virus correlation matrix
the viral correlation analysis includes 66 libraries, and 15 viruses (viruses that appear in at least one of the libraries)
load(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/viruses_load.rds")
# prepare the 'viruses_load' table, with 15 viruses,
# excluding viruses with 'zero tpm': "CBPV", "AFV", "ANV" , "VPVL_46", "VPVL_36", "SBPV", also excluding viruses with low abundance :"KBV", "LSV". left with 15 viruses
viruses_load_15 <- viruses_load %>%
filter(description %in% c("DWVa", "ARV_2","VOV_1", "BMV","AmFV","ABPV","VTLV","IAPV","SV","VDV1/DWVb","DWVc","BQCV","VDV3","VDV2","VDV4")) %>%
column_to_rownames("description") %>%
transposeBigData() %>%
rownames_to_column("library") %>%
#identify and remove the row numbers of the outlierd libraries (found by PCA)
#filter(!(library %in% c("SRR5109825", "SRR5109827", "SRR533974" , "SRR3927496", "SRR8867385"))) %>%
column_to_rownames("library")
# make a function to correlate viruses load
corrplot2 <- function(data,
method = "pearson",
sig.level = 0.05,
order = "original",
diag = FALSE,
type = "upper",
tl.srt = 75,
number.font = 1,
number.cex = 0.5,
mar = c(0, 0, 0, 0)) {
data_incomplete <- data
data <- data[complete.cases(data), ]
mat <- cor(data, method = method)
cor.mtest <- function(mat, method) {
mat <- as.matrix(mat)
n <- ncol(mat)
p.mat <- matrix(NA, n, n)
diag(p.mat) <- 0
for (i in 1:(n - 1)) {
for (j in (i + 1):n) {
tmp <- cor.test(mat[, i], mat[, j], method = method)
p.mat[i, j] <- p.mat[j, i] <- tmp$p.value
}
}
colnames(p.mat) <- rownames(p.mat) <- colnames(mat)
p.mat
}
p.mat <- cor.mtest(data, method = method)
col <- colorRampPalette(c("#053061","#2166ac","#4393c3","#92c5de","#d1e5f0","#f7f7f7","#fddbc7","#f4a582","#d6604d","#b2182b","#67001f"))
corrplot(mat,
method = "color", col = col(200),
mar = mar,
type = type, order = order,
tl.col = "black", # replace with "white" to hide the viruses names, as in the plot for the MS.
# hide correlation coefficients on the diagonal
diag = diag
)
}
# plot the correlogram
virusAbundCor_66 <- corrplot2(
data = viruses_load_15,
method = "pearson",
sig.level = 0.05,
order = "original",
diag = F,
type = "upper",
tl.srt = 75)
Figure 2a. Correlation between viruses’ loads. P-values of the Pearson coefficient are adjusted according to FDR-correction; correlation significance marked by (*) 0.1 < Padjust < 0.01; (**) Padjust < 0.01. All viruses’ loads are transformed by log10 of the (TPM), Transcripts Per Million.
# save the matrix for future analysis (Mantel)
#saveRDS(virusAbundCor_66, file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/virusAbundCor_66.rds")
# and the table of viral load of the 15 viruses in 66 libraries:
#save(viruses_load_15, file = "results/viruses_load_15.rds")Gene network analysis
We used a network analysis approach to identify groups of genes that share a similar expression pattern across a large set of available varroa transcriptomic data (RNAseq). To construct the gene-network, a weighted gene co-expression analysis was carried out using the WGCNA package in R, following the authors’ tutorial (Langfelder and Horvath 2016; Langfelder and Horvath 2008).
The gene network analysis included 4 main steps:
- Network construction and module detection
- Correlating modules to external information, the varroa viral load
- Identifying important genes, ‘hub-genes’
- GO-term enrichment analysis for varroa modules which interact with the viral load
A gene co-expression network is a a systems-biology approach, based on the assumption that biological functions are carried out in a modular manner (Barabási and Oltvai 2004). We identify co-expressed genes that have similar expression patterns across samples using hierarchical clustering and place them in gene groups, called ‘modules’ (Stuart et al. 2003).
(1) Network construction and module detection
Following the steps in WGCNA tutorial: “Automatic, one-step network construction and module detection” (Langfelder and Horvath 2016)
Choosing the soft-thresholding power: analysis of network topology (Figure S1a)
For the varroa Gene network analysis we gonna use the “for_module” file created in the chunk “PCA” of section “Load data and library filtration”. This data frame is the initial input for all the WGCNA, and contains the varroa genes TPM, where columns are genes’ ID and rows are the RNAseq libraries
load(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/for_modules.rds")
# Take a look at the data frame (print 5 genes in 10 libraries):
head(for_modules[,1:5], 10)## 111242787 111242788 111242789 111242790 111242792
## SRR3632582 16.69060 13115.3000 1.632676 4.68461 39.04070
## SRR3633003 27.71050 68.2067 1.006694 8.47756 86.32650
## SRR3634700 30.52360 37.5802 1.105930 7.45524 45.91280
## SRR3634772 39.17820 246.4390 3.671050 9.14239 48.84960
## SRR3634929 12.14060 74095.9000 9.223820 3.01799 20.93230
## SRR3634942 22.61910 12.7722 2.068261 7.35609 51.97150
## SRR3635001 34.69800 19.2896 1.312841 10.61080 58.61030
## SRR3635050 11.08990 85335.2000 9.115974 2.16917 17.92070
## SRR3635105 29.92650 253.0850 2.128474 7.89757 50.31910
## SRR3927486 7.45717 3993.3700 1.491740 1.11916 7.85349# Choose a set of soft-thresholding powers
powers = c(c(1:10), seq(from = 12, to=25, by=2))
# Call the network topology analysis function
sft = pickSoftThreshold(for_modules, powerVector = powers, verbose = 5)## pickSoftThreshold: will use block size 4366.
## pickSoftThreshold: calculating connectivity for given powers...
## ..working on genes 1 through 4366 of 10247
## ..working on genes 4367 through 8732 of 10247
## ..working on genes 8733 through 10247 of 10247
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.84900 1.9000 0.807 3610.0 3730.0 5270
## 2 2 0.54000 0.6600 0.894 1910.0 1920.0 3460
## 3 3 0.00867 -0.0596 0.507 1200.0 1150.0 2540
## 4 4 0.22700 -0.3920 0.527 826.0 820.0 1970
## 5 5 0.35500 -0.6060 0.599 603.0 603.0 1580
## 6 6 0.42100 -0.7390 0.652 459.0 446.0 1300
## 7 7 0.45200 -0.8360 0.675 359.0 337.0 1080
## 8 8 0.49200 -0.8910 0.695 288.0 257.0 916
## 9 9 0.49900 -0.9460 0.682 236.0 199.0 787
## 10 10 0.51500 -0.9400 0.646 196.0 157.0 684
## 11 12 0.88600 -0.8650 0.973 141.0 99.9 557
## 12 14 0.87200 -1.0800 0.922 106.0 66.2 521
## 13 16 0.87100 -1.2100 0.871 82.4 44.8 491
## 14 18 0.86000 -1.2900 0.824 65.9 31.3 465
## 15 20 0.85000 -1.3200 0.809 53.9 22.2 442
## 16 22 0.84800 -1.3300 0.822 45.1 16.2 422
## 17 24 0.84000 -1.3200 0.840 38.4 11.9 404# Plot the results:
sft_df <- data.frame(
Power = sft$fitIndices[,1],
sft_signedR2 = -sign(sft$fitIndices[,3])*sft$fitIndices[,2],
mean.k = sft$fitIndices[,5])
# Scale-free topology fit index as a function of the soft-thresholding power
pSI <- ggplot(data = sft_df, aes(x = Power, y = sft_signedR2, label = Power)) +
xlab("Soft Threshold (power)") +
ylab("Scale Free Topology Model Fit,signed R^2") +
ggtitle("Scale independence") +
theme_classic() +
theme(text = element_text(size=16)) +
geom_text(data = sft_df, aes(x = Power, y = sft_signedR2), size=6) +
geom_hline(yintercept = 0.8, col="red") # this line corresponds to using an R^2 cut-off of h
# Mean connectivity as a function of the soft-thresholding power
pMC <- ggplot(data = sft_df, aes(x = Power, y = mean.k, label = powers)) +
xlab("Soft Threshold (power)") +
ylab("Mean Connectivity") +
ggtitle("Mean Connectivity") +
theme_classic() +
theme(text = element_text(size=16)) +
geom_text(data = sft_df, aes(x = Power, y = mean.k), size=6)
par(mar = c(4, 4, .1, .1))
pSI
pMC
Figure S2a. Network construction using 10,247 genes of 66 SRA varroa libraries. Picking soft threshold.
Constructing the gene network and identifying modules is now a simple function call: (Figure S1b)
net = blockwiseModules(for_modules, power = 12,
TOMType = "unsigned", minModuleSize = 30,
reassignThreshold = 0, mergeCutHeight = 0.25, #0.25 means a correlation of 0.75
numericLabels = TRUE, pamRespectsDendro = FALSE,
#saveTOMs = TRUE,
#saveTOMFileBase = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/Varroa_modulesTOM",
verbose = 3)
# To see how many modules were identified and what the module sizes are, one can use table(net$colors).
table(net$colors)
#saveRDS(net, "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/net.rds")Based on the analysis of network topology, for the construction of the network we set our threshold for merging of modules to 0.25, minimum number of 30 genes per module, and the power β of 12. This power is the lowest for which the scale-free topology fit index curve flattens out upon reaching a high value, in this case, when Rsq reaches 0.886 (Fig S2a). We then performed hierarchical clustering of the genes based on topological overlap (sharing of network neighborhood) to identify groups of genes who coexpressed across libraries, these are the network modules (fig S2b).
The hierarchical clustering dendrogram (tree) used for the module identification is returned in net$dendrograms[[1]]; The dendrogram can be displayed together with the color assignment using the following code
net <- readRDS("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/net.rds")
# Convert labels to colors for plotting
mergedColors = labels2colors(net$colors)
# Plot the dendrogram and the module colors underneath
plotDendroAndColors(net$dendrograms[[1]], mergedColors[net$blockGenes[[1]]],
"Module colors",
dendroLabels = FALSE, hang = 0.03,
addGuide = TRUE, guideHang = 0.05)
Figure S2b. Network construction using 10,247 genes of 66 SRA varroa libraries. Hierarchical clustering dendrogram using merge cut height of 25%, revealing 15 co-expressed genes modules. Each branch of the dendrogram represents a single gene, and the colored bar below denotes its corresponding module, as annotated in the legend to the right. The dendrogram height is the distance between genes.
Save the module assignment and module eigengene information necessary for subsequent analysis:
moduleLabels = net$colors
moduleColors = labels2colors(net$colors)
MEs = net$MEs;
geneTree = net$dendrograms[[1]];
#save(MEs, moduleLabels, moduleColors, geneTree, file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/Varroa_modules_networkConstruction-auto.RData")(2) Figure 2b. Correlating modules to viral load
To test if the varroa modules interact with the different viruses it carries, we correlated the module eigengenes to the viruses’ load (log10TPM). We used Pearson correlation method and adjusted the p-values for multiple comparisons using the Benjamini–Hochberg method to control the false discovery rate (Benjamini and Hochberg 1995) (Fig 2b).
# For correlating varroa modules to viral load, we gonna use the table of 15 viruses saved in chunk "viral correlation", in section "viral correlation matrix", and correlated these to the varroa modules eigengenes found in the previous chunk.
# First we load the two data:
load("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/viruses_load_15.rds")
# change the names of the viruses to match their common name in the literature:
viruses_load_15 <- viruses_load_15 %>%
dplyr::rename("VOV-1" = "VOV_1", "ARV-2"= "ARV_2", "SBV"= "SV", "DWVb"="VDV1/DWVb")
load(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/Varroa_modules_networkConstruction-auto.RData")
load(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/for_modules.rds")
# Define numbers of genes and samples
nGenes = ncol(for_modules);
nSamples = nrow(for_modules)
# Recalculate MEs with color labels
MEs0 = moduleEigengenes(for_modules, moduleColors)$eigengenes
MEs = orderMEs(MEs0)
# correlate the modules eigengenes (MEs) with the viral load (viruses_load_15)
moduleTraitCor_66 = cor(MEs, viruses_load_15, use = "p") %>%
as.matrix()
moduleTraitPvalue = corPvalueStudent(moduleTraitCor_66, nSamples)
### Controlling the false discovery rate: Benjamini–Hochberg procedure ###
# using p.adjust function, for all comparisons, 15 modules and 15 viruses (m=225).
# first make the p-value matrix into a dataframe
moduleTraitPvalue_0 <- as.data.frame(moduleTraitPvalue)
# then "gather" all the p-values, so they will apear in one column
longer_Pvalue <- moduleTraitPvalue_0 %>%
rownames_to_column("module") %>%
gather("virus", "pvalue", -module)
# now calculate the p.adjust for each p-value
Padjust <- p.adjust(longer_Pvalue$pvalue, method = "fdr")
# and add the column of adjusted pvalues
Padjust <- add_column(longer_Pvalue, Padjust)
# now spread it back
moduleTraitPadjust <- Padjust %>%
dplyr::select(-pvalue) %>%
group_by(virus) %>%
pivot_wider(names_from = virus, values_from = Padjust)
moduleTraitPadjust <- column_to_rownames(moduleTraitPadjust, "module") %>%
as.matrix()# Display correlations and their adjusted p-values
textMatrix = paste(signif(moduleTraitCor_66, 2), "\n(",
signif(moduleTraitPadjust, 1), ")", sep = "");
dim(textMatrix) = dim(moduleTraitCor_66)
par(mar = c(6, 8.5, 3, 3));
# Display the correlation values within a heatmap plot
labeledHeatmap(Matrix = moduleTraitCor_66,
xLabels = names(viruses_load_15),
yLabels = names(MEs),
#xLabelsAngle = 90,
ySymbols = names(MEs),
colorLabels = FALSE,
colors = hcl.colors(n = 50, palette = "RdBu", alpha = NULL, rev = FALSE, fixup = TRUE),
invertColors = TRUE,
textMatrix = textMatrix,
setStdMargins = FALSE,
cex.text = 0.7,
zlim = c(-1,1),
main = paste("Varroa Module-viruses relationships"))
Figure 2b. Correlation between viruses’ loads and varroa modules (eigengenes). Viruses and modules are ordered according to hierarchical clustering; P-values of the Pearson coefficient are adjusted according to FDR-correction. In each cell, module-virus correlation values are given: Pearson correlation coefficient (up) and adjusted P-value.
# save the matrices for next analyses
#save(moduleTraitCor_66,moduleTraitPadjust_66, file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/moduleTraitCor_66.RData")Correlating varroa modules eigengenes to their viruses’ loads (transcript per million, TPM), we found significant interactions between specific modules and viruses (Pearson correlation followed by Benjamini-Hochberg FDR-correction, P-adjust < 0.1, Fig 2b).
| Module number | Module color |
|---|---|
| MM.0 | MM.grey |
| MM.1 | MM.turquoise |
| MM.2 | MM.blue |
| MM.3 | MM.brown |
| MM.4 | MM.yellow |
| MM.5 | MM.green |
| MM.6 | MM.red |
| MM.7 | MM.black |
| MM.8 | MM.pink |
| MM.9 | MM.magenta |
| MM.10 | MM.purple |
| MM.11 | MM.greenyellow |
| MM.1 | MM.tan |
| MM.13 | MM.salmon |
| MM.14 | MM.cyan |
| MM.15 | MM.midnightblue |
(3) Identifying important genes
The important genes were identified according to their Module membership (Langfelder and Horvath 2008), and their annotation (based on sequence similarity to homologue genes). A gene Module membership expresses its connection to other genes in the module, and therefore, measures the extent to which this gene represents the overall module. The Module membership is calculated by Pearson correlation of the module eigengene and the gene expression. Genes with high Module membership and relevant annotation are likely to play a role in the vector-virus interaction, and are good candidates for later experimental validation.
Calculating gene Module-membership (MM)
# names (colors) of the modules
modNames = substring(names(MEs), 3)
# virusNames = substring(names(viruses_load_15), 1)
#make a table of the Module-membership ("MM") of each gene (which is its correlation coefficient, pearson)
geneModuleMembership_66 = as.data.frame(cor(for_modules, MEs, use = "p"));
MMPvalue_66 = as.data.frame(corPvalueStudent(as.matrix(geneModuleMembership_66), nSamples));
### Controlling the false discovery rate: Benjamini–Hochberg procedure ###
# using p.adjust function, for all comparisons, 15 modules and 15 viruses (m=225).
# first make the p-value matrix into a dataframe
MMPvalue_66_0 <- as.data.frame(MMPvalue_66)
# then "gather" all the p-values, so they will appear in one column
longer_Pvalue <- MMPvalue_66_0 %>%
rownames_to_column("module") %>%
gather("virus", "pvalue", -module)
# now calculate the p.adjust for each p-value
Padjust <- p.adjust(longer_Pvalue$pvalue, method = "fdr")
# and add the column of adjusted pvalues
Padjust <- add_column(longer_Pvalue, Padjust)
# now spread it back
MMPadjust_66 <- Padjust %>%
dplyr::select(-pvalue) %>%
group_by(virus) %>%
pivot_wider(names_from = virus, values_from = Padjust)
MMPadjust_66 <- column_to_rownames(MMPadjust_66, "module")
#change the name of the columns to start with "MM" then the module name
names(geneModuleMembership_66) = paste("MM", modNames, sep="");
names(MMPadjust_66) = paste("padj.MM", modNames, sep="");Identifying genes with high Module-membership in module 10 (the purple module) and adding gene annotations
genePurple = data.frame(
moduleCol = moduleColors,
geneModuleMembership_66,
MMPadjust_66) %>%
dplyr::select(c(moduleCol, MMpurple, padj.MMpurple)) %>%
dplyr::filter(moduleCol == "purple") %>%
mutate(moduleNum = "Module.10") %>%
rownames_to_column("genes")
# add gene annotation:
# load the annotation file:
annot_varroa <- read_csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/data/annot_varroa.csv", col_names = TRUE, )
# remove the "LOC" from the gene name
annot_varroa$Locus <- str_replace(annot_varroa$Locus, "LOC", '')
# change the col name to "genes", so it will the same as in the "overlap" table
colnames(annot_varroa)[which(names(annot_varroa) == "Locus")] <- "genes"
head(annot_varroa)## # A tibble: 6 x 11
## Name Accession Start Stop Strand GeneID genes `Locus tag` `Protein produc…
## <chr> <chr> <dbl> <dbl> <chr> <dbl> <chr> <chr> <chr>
## 1 Un NW_01921… 3.38e7 3.39e7 - 1.11e8 1112… - XP_022672900.1
## 2 Un NW_01921… 3.38e7 3.39e7 - 1.11e8 1112… - XP_022672902.1
## 3 Un NW_01921… 3.38e7 3.39e7 - 1.11e8 1112… - XP_022672903.1
## 4 Un NW_01921… 3.38e7 3.39e7 - 1.11e8 1112… - XP_022672904.1
## 5 Un NW_01921… 3.38e7 3.39e7 - 1.11e8 1112… - XP_022672905.1
## 6 Un NW_01921… 3.38e7 3.39e7 - 1.11e8 1112… - XP_022672908.1
## # … with 2 more variables: Length <dbl>, Protein Name <chr>genesModule.10 <- left_join(annot_varroa, genePurple, by = "genes") %>%
na.omit() %>%
dplyr::select("genes", "moduleNum", "MMpurple", "padj.MMpurple", "Accession", "Protein Name") %>%
dplyr::rename(c(MM = MMpurple, MMpadj = padj.MMpurple))
# there are total of 263 matching annotations, as some of the genes have a few isoforms.
# save the final table of the genes in module 10
write_csv(genesModule.10, "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/genesModule.10.csv")Identifying genes with high Module-membership in module 9
Identifying genes with high Module-membership in module 6
Identifying genes with high Module-membership in module 3
Calculating Gene Significanse (GS)
# save(geneTraitSignificance_66, GSPadjust_66, geneModuleMembership_66, MMPadjust_66, file = "/results/geneTraitANDgeneMM_66.RData")(4) GO-term enrichment analysis for varroa modules (Tables S2-S10)
Analysis based on Tehcer et al. (2019)
# load the annotation table of Varroa destructor
annot.vd <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/data/VdesGOready2.csv")
#Preparing the GO frame
annot.vd2 <- annot.vd %>%
mutate(evidence = "IEA") %>%
dplyr::select(go_id = GO.ids, evidence, gene = Gene.id)
#head(annot.vd2)
goFrame.vd <-GOFrame(annot.vd2, organism = "Vd")
goAllFrame.vd <-GOAllFrame(goFrame.vd)
gsc.vd <-GeneSetCollection(goAllFrame.vd, setType = GOCollection())
#Preparing the universe
universe.vd <- as.character(unique(annot.vd2$gene)) # there's a wired thing in the GSEAGOHyperGParams function, sometimes its required the universe to be "character".
#head(universe.vd)
# Preparing the gene set (list of genes in a module)
# change "black" to the name of the desired module, in the first line: [moduleColors=="black"], and in the final "write.csv(file = "GO_term_enrichment_**salmon**BP.csv")
ME <- names(for_modules)[moduleColors=="black"]
ME_df <- data.frame(gene = ME)
genes.vd <- unique(ME_df$gene)
head(genes.vd)## [1] "111242800" "111242844" "111242861" "111242884" "111242885" "111242988"params.vd <- GSEAGOHyperGParams(name = "Vd_GO_enrichment",
geneSetCollection = gsc.vd,
geneIds = genes.vd,
universeGeneIds = universe.vd,
ontology = "BP", # change with MF, CC to test all
pvalueCutoff = 0.05,
conditional = F,
testDirection = "over")
over.vd <- hyperGTest(params.vd)
#over.vd
#summary(over.vd)
GO_enrich.vd <- as.data.frame(summary(over.vd)) %>%
arrange(Pvalue)
# write.csv(GO_enrich.vd, file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_black.csv")All GO-terms of the significantly interacting modules are also available as csv files, on the github project result folder
Significant GO-terms of the interacting modules
Module 1
GO_term_turquoise <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_turquoise.csv")
GO_term_turquoise %>%
kbl() %>%
kable_styling(bootstrap_options = "striped", full_width = F, position = "left") %>%
kable_paper() %>%
scroll_box(width = "800px", height = "200px")| X | GOBPID | Pvalue | OddsRatio | ExpCount | Count | Size | Term |
|---|---|---|---|---|---|---|---|
| 1 | GO:0043043 | 0.0000000 | 5.007628 | 97.968685 | 184 | 242 | peptide biosynthetic process |
| 2 | GO:0006412 | 0.0000000 | 5.036588 | 96.754197 | 182 | 239 | translation |
| 3 | GO:0043604 | 0.0000000 | 4.617744 | 103.231466 | 190 | 255 | amide biosynthetic process |
| 4 | GO:0006518 | 0.0000000 | 4.376512 | 109.708734 | 199 | 271 | peptide metabolic process |
| 5 | GO:0043603 | 0.0000000 | 3.590242 | 123.068100 | 211 | 304 | cellular amide metabolic process |
| 6 | GO:0034641 | 0.0000000 | 1.859933 | 684.161479 | 858 | 1690 | cellular nitrogen compound metabolic process |
| 7 | GO:1901566 | 0.0000000 | 2.429725 | 208.487078 | 310 | 515 | organonitrogen compound biosynthetic process |
| 8 | GO:0034660 | 0.0000000 | 4.251384 | 70.035465 | 127 | 173 | ncRNA metabolic process |
| 9 | GO:0006396 | 0.0000000 | 2.873901 | 117.400491 | 188 | 290 | RNA processing |
| 10 | GO:0022613 | 0.0000000 | 5.417015 | 46.150538 | 89 | 114 | ribonucleoprotein complex biogenesis |
| 11 | GO:0042254 | 0.0000000 | 8.029258 | 33.196001 | 69 | 82 | ribosome biogenesis |
| 12 | GO:0044237 | 0.0000000 | 1.578136 | 1168.742124 | 1312 | 2887 | cellular metabolic process |
| 13 | GO:0006807 | 0.0000000 | 1.569641 | 1133.521977 | 1276 | 2800 | nitrogen compound metabolic process |
| 14 | GO:0034470 | 0.0000000 | 4.565027 | 50.198830 | 93 | 124 | ncRNA processing |
| 15 | GO:0010467 | 0.0000000 | 1.612678 | 525.468402 | 640 | 1298 | gene expression |
| 16 | GO:0008152 | 0.0000000 | 1.563687 | 1438.358423 | 1562 | 3553 | metabolic process |
| 17 | GO:0071704 | 0.0000000 | 1.518342 | 1272.783248 | 1400 | 3144 | organic substance metabolic process |
| 18 | GO:0044238 | 0.0000000 | 1.502527 | 1209.225052 | 1336 | 2987 | primary metabolic process |
| 19 | GO:0043170 | 0.0000000 | 1.488247 | 1020.574609 | 1147 | 2521 | macromolecule metabolic process |
| 20 | GO:0006399 | 0.0000000 | 4.418506 | 41.292586 | 76 | 102 | tRNA metabolic process |
| 21 | GO:0006725 | 0.0000000 | 1.479120 | 594.694209 | 696 | 1469 | cellular aromatic compound metabolic process |
| 22 | GO:0046483 | 0.0000000 | 1.464680 | 594.289379 | 693 | 1468 | heterocycle metabolic process |
| 23 | GO:1901360 | 0.0000000 | 1.443885 | 610.482551 | 707 | 1508 | organic cyclic compound metabolic process |
| 24 | GO:0006139 | 0.0000000 | 1.447993 | 576.072062 | 670 | 1423 | nucleobase-containing compound metabolic process |
| 25 | GO:0008033 | 0.0000000 | 5.133052 | 25.099415 | 48 | 62 | tRNA processing |
| 26 | GO:0006259 | 0.0000000 | 2.128167 | 92.301075 | 133 | 228 | DNA metabolic process |
| 27 | GO:0044267 | 0.0000000 | 1.432762 | 480.127523 | 561 | 1186 | cellular protein metabolic process |
| 28 | GO:0006974 | 0.0000000 | 2.280997 | 74.083758 | 110 | 183 | cellular response to DNA damage stimulus |
| 29 | GO:0009451 | 0.0000001 | 4.072299 | 27.123562 | 49 | 67 | RNA modification |
| 30 | GO:0016072 | 0.0000001 | 4.824656 | 22.265610 | 42 | 55 | rRNA metabolic process |
| 31 | GO:0006364 | 0.0000001 | 5.290417 | 20.241464 | 39 | 50 | rRNA processing |
| 32 | GO:0033554 | 0.0000001 | 1.860501 | 127.521222 | 173 | 315 | cellular response to stress |
| 33 | GO:0008380 | 0.0000001 | 3.150504 | 37.649123 | 63 | 93 | RNA splicing |
| 34 | GO:0090304 | 0.0000001 | 1.405291 | 504.822109 | 584 | 1247 | nucleic acid metabolic process |
| 35 | GO:0044249 | 0.0000004 | 1.365788 | 573.238257 | 652 | 1416 | cellular biosynthetic process |
| 36 | GO:0009057 | 0.0000005 | 1.953867 | 92.705905 | 129 | 229 | macromolecule catabolic process |
| 37 | GO:0044265 | 0.0000009 | 2.063378 | 75.703075 | 108 | 187 | cellular macromolecule catabolic process |
| 38 | GO:0009058 | 0.0000012 | 1.341800 | 598.742501 | 675 | 1479 | biosynthetic process |
| 39 | GO:0006400 | 0.0000013 | 6.687353 | 13.359366 | 27 | 33 | tRNA modification |
| 40 | GO:1901576 | 0.0000014 | 1.342540 | 583.763818 | 659 | 1442 | organic substance biosynthetic process |
| 41 | GO:0006260 | 0.0000016 | 2.937504 | 33.600830 | 55 | 83 | DNA replication |
| 42 | GO:0030163 | 0.0000022 | 2.063498 | 70.035465 | 100 | 173 | protein catabolic process |
| 43 | GO:0044260 | 0.0000030 | 1.300215 | 806.015092 | 885 | 1991 | cellular macromolecule metabolic process |
| 44 | GO:0044257 | 0.0000043 | 2.236931 | 53.437465 | 79 | 132 | cellular protein catabolic process |
| 45 | GO:0051603 | 0.0000043 | 2.236931 | 53.437465 | 79 | 132 | proteolysis involved in cellular protein catabolic process |
| 46 | GO:0019538 | 0.0000054 | 1.321495 | 570.809281 | 641 | 1410 | protein metabolic process |
| 47 | GO:0006281 | 0.0000065 | 2.220796 | 52.222977 | 77 | 129 | DNA repair |
| 48 | GO:1901565 | 0.0000080 | 1.819851 | 91.086587 | 123 | 225 | organonitrogen compound catabolic process |
| 49 | GO:0000398 | 0.0000106 | 2.812094 | 30.362196 | 49 | 75 | mRNA splicing, via spliceosome |
| 50 | GO:0000375 | 0.0000106 | 2.812094 | 30.362196 | 49 | 75 | RNA splicing, via transesterification reactions |
| 51 | GO:0000377 | 0.0000106 | 2.812094 | 30.362196 | 49 | 75 | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile |
| 52 | GO:0016071 | 0.0000120 | 2.032743 | 61.938879 | 88 | 153 | mRNA metabolic process |
| 53 | GO:0034645 | 0.0000123 | 1.330952 | 467.982645 | 531 | 1156 | cellular macromolecule biosynthetic process |
| 54 | GO:1901564 | 0.0000126 | 1.286134 | 705.617431 | 777 | 1743 | organonitrogen compound metabolic process |
| 55 | GO:0140053 | 0.0000133 | 12.588304 | 7.691756 | 17 | 19 | mitochondrial gene expression |
| 56 | GO:0006520 | 0.0000154 | 2.334716 | 42.507074 | 64 | 105 | cellular amino acid metabolic process |
| 57 | GO:0009056 | 0.0000172 | 1.543975 | 164.765516 | 205 | 407 | catabolic process |
| 58 | GO:0009059 | 0.0000177 | 1.322441 | 472.030938 | 534 | 1166 | macromolecule biosynthetic process |
| 59 | GO:1901575 | 0.0000214 | 1.588293 | 140.070930 | 177 | 346 | organic substance catabolic process |
| 60 | GO:0043632 | 0.0000232 | 2.196826 | 46.960196 | 69 | 116 | modification-dependent macromolecule catabolic process |
| 61 | GO:0051186 | 0.0000234 | 2.227246 | 45.340879 | 67 | 112 | cofactor metabolic process |
| 62 | GO:0044248 | 0.0000263 | 1.568512 | 144.928881 | 182 | 358 | cellular catabolic process |
| 63 | GO:0022618 | 0.0000291 | 3.658540 | 18.217318 | 32 | 45 | ribonucleoprotein complex assembly |
| 64 | GO:0043038 | 0.0000323 | 4.157696 | 15.383513 | 28 | 38 | amino acid activation |
| 65 | GO:0043039 | 0.0000323 | 4.157696 | 15.383513 | 28 | 38 | tRNA aminoacylation |
| 66 | GO:0006418 | 0.0000323 | 4.157696 | 15.383513 | 28 | 38 | tRNA aminoacylation for protein translation |
| 67 | GO:0019941 | 0.0000351 | 2.178127 | 45.745708 | 67 | 113 | modification-dependent protein catabolic process |
| 68 | GO:0006511 | 0.0000351 | 2.178127 | 45.745708 | 67 | 113 | ubiquitin-dependent protein catabolic process |
| 69 | GO:0006397 | 0.0000356 | 2.208455 | 44.126391 | 65 | 109 | mRNA processing |
| 70 | GO:0071826 | 0.0000588 | 3.396135 | 18.622147 | 32 | 46 | ribonucleoprotein complex subunit organization |
| 71 | GO:0032543 | 0.0000658 | 11.096903 | 6.882098 | 15 | 17 | mitochondrial translation |
| 72 | GO:0006457 | 0.0000843 | 2.278880 | 36.839464 | 55 | 91 | protein folding |
| 73 | GO:0006790 | 0.0001323 | 2.971591 | 20.646293 | 34 | 51 | sulfur compound metabolic process |
| 74 | GO:0042273 | 0.0001447 | 10.352251 | 6.477268 | 14 | 16 | ribosomal large subunit biogenesis |
| 75 | GO:0001522 | 0.0001552 | 17.735708 | 5.262781 | 12 | 13 | pseudouridine synthesis |
| 76 | GO:0000278 | 0.0003636 | 1.853689 | 52.627806 | 72 | 130 | mitotic cell cycle |
| 77 | GO:0044271 | 0.0003786 | 1.261487 | 449.360498 | 499 | 1110 | cellular nitrogen compound biosynthetic process |
| 78 | GO:0009987 | 0.0004146 | 1.248263 | 1621.341256 | 1673 | 4005 | cellular process |
| 79 | GO:0043436 | 0.0004773 | 1.620858 | 82.585173 | 106 | 204 | oxoacid metabolic process |
| 80 | GO:0006082 | 0.0004773 | 1.620858 | 82.585173 | 106 | 204 | organic acid metabolic process |
| 81 | GO:0006779 | 0.0007158 | Inf | 3.238634 | 8 | 8 | porphyrin-containing compound biosynthetic process |
| 82 | GO:0006415 | 0.0008130 | 14.765918 | 4.453122 | 10 | 11 | translational termination |
| 83 | GO:0006778 | 0.0008130 | 14.765918 | 4.453122 | 10 | 11 | porphyrin-containing compound metabolic process |
| 84 | GO:0019752 | 0.0008225 | 1.588718 | 81.775514 | 104 | 202 | carboxylic acid metabolic process |
| 85 | GO:0006950 | 0.0009121 | 1.345459 | 206.462931 | 240 | 510 | response to stress |
| 86 | GO:0000086 | 0.0010573 | 6.403500 | 6.477268 | 13 | 16 | G2/M transition of mitotic cell cycle |
| 87 | GO:0007049 | 0.0010597 | 1.488883 | 106.470100 | 131 | 263 | cell cycle |
| 88 | GO:0045184 | 0.0010800 | 1.469529 | 113.757027 | 139 | 281 | establishment of protein localization |
| 89 | GO:0007005 | 0.0012181 | 1.923275 | 38.053952 | 53 | 94 | mitochondrion organization |
| 90 | GO:0071840 | 0.0012356 | 1.241832 | 408.877570 | 452 | 1010 | cellular component organization or biogenesis |
| 91 | GO:0006611 | 0.0014467 | 5.172842 | 7.286927 | 14 | 18 | protein export from nucleus |
| 92 | GO:0042255 | 0.0014628 | 8.122482 | 5.262781 | 11 | 13 | ribosome assembly |
| 93 | GO:0044272 | 0.0018290 | 4.434538 | 8.096585 | 15 | 20 | sulfur compound biosynthetic process |
| 94 | GO:0000387 | 0.0018405 | 13.283107 | 4.048293 | 9 | 10 | spliceosomal snRNP assembly |
| 95 | GO:0090150 | 0.0019263 | 3.108000 | 12.549708 | 21 | 31 | establishment of protein localization to membrane |
| 96 | GO:0033013 | 0.0021524 | 5.908154 | 6.072439 | 12 | 15 | tetrapyrrole metabolic process |
| 97 | GO:0006261 | 0.0022931 | 2.733560 | 14.978683 | 24 | 37 | DNA-dependent DNA replication |
| 98 | GO:0006886 | 0.0023134 | 1.524627 | 80.156197 | 100 | 198 | intracellular protein transport |
| 99 | GO:0016070 | 0.0023557 | 1.218765 | 434.786644 | 476 | 1074 | RNA metabolic process |
| 100 | GO:1903047 | 0.0024989 | 1.755582 | 44.126391 | 59 | 109 | mitotic cell cycle process |
| 101 | GO:0007346 | 0.0025679 | 2.192194 | 23.075269 | 34 | 57 | regulation of mitotic cell cycle |
| 102 | GO:0072527 | 0.0028261 | 4.801102 | 6.882098 | 13 | 17 | pyrimidine-containing compound metabolic process |
| 103 | GO:0072594 | 0.0028737 | 1.897804 | 33.196001 | 46 | 82 | establishment of protein localization to organelle |
| 104 | GO:0042278 | 0.0030960 | 7.380618 | 4.857951 | 10 | 12 | purine nucleoside metabolic process |
| 105 | GO:0042886 | 0.0034006 | 1.419737 | 107.279758 | 129 | 265 | amide transport |
| 106 | GO:0006605 | 0.0034637 | 1.995221 | 27.528391 | 39 | 68 | protein targeting |
| 107 | GO:0015031 | 0.0035530 | 1.418933 | 106.470100 | 128 | 263 | protein transport |
| 108 | GO:0045454 | 0.0039790 | 2.406073 | 17.002830 | 26 | 42 | cell redox homeostasis |
| 109 | GO:0048364 | 0.0041292 | 11.801684 | 3.643464 | 8 | 9 | root development |
| 110 | GO:0031145 | 0.0041292 | 11.801684 | 3.643464 | 8 | 9 | anaphase-promoting complex-dependent catabolic process |
| 111 | GO:0022622 | 0.0041292 | 11.801684 | 3.643464 | 8 | 9 | root system development |
| 112 | GO:0015833 | 0.0041983 | 1.408034 | 106.874929 | 128 | 264 | peptide transport |
| 113 | GO:0042274 | 0.0043216 | 5.413271 | 5.667610 | 11 | 14 | ribosomal small subunit biogenesis |
| 114 | GO:0097300 | 0.0043835 | Inf | 2.428976 | 6 | 6 | programmed necrotic cell death |
| 115 | GO:1901990 | 0.0049208 | 3.141087 | 10.120732 | 17 | 25 | regulation of mitotic cell cycle phase transition |
| 116 | GO:0071426 | 0.0054379 | 4.429710 | 6.477268 | 12 | 16 | ribonucleoprotein complex export from nucleus |
| 117 | GO:0071166 | 0.0054379 | 4.429710 | 6.477268 | 12 | 16 | ribonucleoprotein complex localization |
| 118 | GO:0006289 | 0.0054379 | 4.429710 | 6.477268 | 12 | 16 | nucleotide-excision repair |
| 119 | GO:0044281 | 0.0054737 | 1.293010 | 182.982833 | 209 | 452 | small molecule metabolic process |
| 120 | GO:1903827 | 0.0056830 | 2.037447 | 23.075269 | 33 | 57 | regulation of cellular protein localization |
| 121 | GO:0033365 | 0.0060184 | 1.614970 | 48.984343 | 63 | 121 | protein localization to organelle |
| 122 | GO:1903829 | 0.0060863 | 2.503404 | 14.169025 | 22 | 35 | positive regulation of cellular protein localization |
| 123 | GO:0044839 | 0.0064124 | 3.839662 | 7.286927 | 13 | 18 | cell cycle G2/M phase transition |
| 124 | GO:0000413 | 0.0064124 | 3.839662 | 7.286927 | 13 | 18 | protein peptidyl-prolyl isomerization |
| 125 | GO:0031570 | 0.0064124 | 3.839662 | 7.286927 | 13 | 18 | DNA integrity checkpoint |
| 126 | GO:0018208 | 0.0064124 | 3.839662 | 7.286927 | 13 | 18 | peptidyl-proline modification |
| 127 | GO:0006220 | 0.0064646 | 6.639448 | 4.453122 | 9 | 11 | pyrimidine nucleotide metabolic process |
| 128 | GO:0044085 | 0.0069782 | 1.275013 | 192.293907 | 218 | 475 | cellular component biogenesis |
| 129 | GO:0051188 | 0.0070292 | 1.877767 | 27.528391 | 38 | 68 | cofactor biosynthetic process |
| 130 | GO:0006414 | 0.0072378 | 3.446373 | 8.096585 | 14 | 20 | translational elongation |
| 131 | GO:0043161 | 0.0079183 | 1.937391 | 24.289757 | 34 | 60 | proteasome-mediated ubiquitin-dependent protein catabolic process |
| 132 | GO:0042180 | 0.0079195 | 3.165516 | 8.906244 | 15 | 22 | cellular ketone metabolic process |
| 133 | GO:0048193 | 0.0081380 | 1.955324 | 23.480098 | 33 | 58 | Golgi vesicle transport |
| 134 | GO:0000077 | 0.0085402 | 4.918851 | 5.262781 | 10 | 13 | DNA damage checkpoint |
| 135 | GO:0033014 | 0.0085402 | 4.918851 | 5.262781 | 10 | 13 | tetrapyrrole biosynthetic process |
| 136 | GO:0031398 | 0.0088998 | 2.791190 | 10.525561 | 17 | 26 | positive regulation of protein ubiquitination |
| 137 | GO:1903322 | 0.0088998 | 2.791190 | 10.525561 | 17 | 26 | positive regulation of protein modification by small protein conjugation or removal |
| 138 | GO:0070265 | 0.0091623 | 10.321646 | 3.238634 | 7 | 8 | necrotic cell death |
| 139 | GO:0006739 | 0.0091623 | 10.321646 | 3.238634 | 7 | 8 | NADP metabolic process |
| 140 | GO:1901987 | 0.0092262 | 2.660244 | 11.335220 | 18 | 28 | regulation of cell cycle phase transition |
| 141 | GO:0099402 | 0.0102868 | 4.058665 | 6.072439 | 11 | 15 | plant organ development |
| 142 | GO:0042168 | 0.0108431 | Inf | 2.024146 | 5 | 5 | heme metabolic process |
| 143 | GO:0010053 | 0.0108431 | Inf | 2.024146 | 5 | 5 | root epidermal cell differentiation |
| 144 | GO:0017004 | 0.0108431 | Inf | 2.024146 | 5 | 5 | cytochrome complex assembly |
| 145 | GO:0010015 | 0.0108431 | Inf | 2.024146 | 5 | 5 | root morphogenesis |
| 146 | GO:0007398 | 0.0108431 | Inf | 2.024146 | 5 | 5 | ectoderm development |
| 147 | GO:0000394 | 0.0108431 | Inf | 2.024146 | 5 | 5 | RNA splicing, via endonucleolytic cleavage and ligation |
| 148 | GO:0000463 | 0.0108431 | Inf | 2.024146 | 5 | 5 | maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) |
| 149 | GO:0000470 | 0.0108431 | Inf | 2.024146 | 5 | 5 | maturation of LSU-rRNA |
| 150 | GO:0097039 | 0.0108431 | Inf | 2.024146 | 5 | 5 | protein linear polyubiquitination |
| 151 | GO:0070266 | 0.0108431 | Inf | 2.024146 | 5 | 5 | necroptotic process |
| 152 | GO:0007220 | 0.0108431 | Inf | 2.024146 | 5 | 5 | Notch receptor processing |
| 153 | GO:0033146 | 0.0108431 | Inf | 2.024146 | 5 | 5 | regulation of intracellular estrogen receptor signaling pathway |
| 154 | GO:0009067 | 0.0108431 | Inf | 2.024146 | 5 | 5 | aspartate family amino acid biosynthetic process |
| 155 | GO:0010992 | 0.0108431 | Inf | 2.024146 | 5 | 5 | ubiquitin recycling |
| 156 | GO:0010994 | 0.0108431 | Inf | 2.024146 | 5 | 5 | free ubiquitin chain polymerization |
| 157 | GO:0090558 | 0.0108431 | Inf | 2.024146 | 5 | 5 | plant epidermis development |
| 158 | GO:0090627 | 0.0108431 | Inf | 2.024146 | 5 | 5 | plant epidermal cell differentiation |
| 159 | GO:1901068 | 0.0108431 | Inf | 2.024146 | 5 | 5 | guanosine-containing compound metabolic process |
| 160 | GO:0009226 | 0.0108431 | Inf | 2.024146 | 5 | 5 | nucleotide-sugar biosynthetic process |
| 161 | GO:0009733 | 0.0108431 | Inf | 2.024146 | 5 | 5 | response to auxin |
| 162 | GO:0006098 | 0.0108431 | Inf | 2.024146 | 5 | 5 | pentose-phosphate shunt |
| 163 | GO:0030520 | 0.0108431 | Inf | 2.024146 | 5 | 5 | intracellular estrogen receptor signaling pathway |
| 164 | GO:0019682 | 0.0108431 | Inf | 2.024146 | 5 | 5 | glyceraldehyde-3-phosphate metabolic process |
| 165 | GO:0006388 | 0.0108431 | Inf | 2.024146 | 5 | 5 | tRNA splicing, via endonucleolytic cleavage and ligation |
| 166 | GO:0051156 | 0.0108431 | Inf | 2.024146 | 5 | 5 | glucose 6-phosphate metabolic process |
| 167 | GO:1901570 | 0.0108431 | Inf | 2.024146 | 5 | 5 | fatty acid derivative biosynthetic process |
| 168 | GO:0006783 | 0.0108431 | Inf | 2.024146 | 5 | 5 | heme biosynthetic process |
| 169 | GO:0006544 | 0.0108431 | Inf | 2.024146 | 5 | 5 | glycine metabolic process |
| 170 | GO:0016073 | 0.0117062 | 3.542643 | 6.882098 | 12 | 17 | snRNA metabolic process |
| 171 | GO:0051028 | 0.0117062 | 3.542643 | 6.882098 | 12 | 17 | mRNA transport |
| 172 | GO:0044770 | 0.0125040 | 1.930632 | 21.455952 | 30 | 53 | cell cycle phase transition |
| 173 | GO:0006633 | 0.0128275 | 3.198703 | 7.691756 | 13 | 19 | fatty acid biosynthetic process |
| 174 | GO:0010498 | 0.0129994 | 1.759280 | 28.338049 | 38 | 70 | proteasomal protein catabolic process |
| 175 | GO:0051187 | 0.0132838 | 5.898971 | 4.048293 | 8 | 10 | cofactor catabolic process |
| 176 | GO:1901661 | 0.0132838 | 5.898971 | 4.048293 | 8 | 10 | quinone metabolic process |
| 177 | GO:0090501 | 0.0136883 | 2.953096 | 8.501415 | 14 | 21 | RNA phosphodiester bond hydrolysis |
| 178 | GO:0009267 | 0.0136883 | 2.953096 | 8.501415 | 14 | 21 | cellular response to starvation |
| 179 | GO:0043933 | 0.0147306 | 1.324910 | 109.303905 | 127 | 270 | protein-containing complex subunit organization |
| 180 | GO:0051168 | 0.0147767 | 2.625769 | 10.120732 | 16 | 25 | nuclear export |
| 181 | GO:0044283 | 0.0148824 | 1.537202 | 46.150538 | 58 | 114 | small molecule biosynthetic process |
| 182 | GO:0000075 | 0.0152319 | 2.417635 | 11.740049 | 18 | 29 | cell cycle checkpoint |
| 183 | GO:0019725 | 0.0155556 | 1.574099 | 40.887757 | 52 | 101 | cellular homeostasis |
| 184 | GO:0006732 | 0.0165605 | 1.699084 | 29.552537 | 39 | 73 | coenzyme metabolic process |
| 185 | GO:0048229 | 0.0165701 | 4.424895 | 4.857951 | 9 | 12 | gametophyte development |
| 186 | GO:0010389 | 0.0165701 | 4.424895 | 4.857951 | 9 | 12 | regulation of G2/M transition of mitotic cell cycle |
| 187 | GO:0033143 | 0.0165701 | 4.424895 | 4.857951 | 9 | 12 | regulation of intracellular steroid hormone receptor signaling pathway |
| 188 | GO:0072528 | 0.0165701 | 4.424895 | 4.857951 | 9 | 12 | pyrimidine-containing compound biosynthetic process |
| 189 | GO:0008104 | 0.0174754 | 1.259311 | 155.859272 | 176 | 385 | protein localization |
| 190 | GO:0009119 | 0.0190866 | 3.687968 | 5.667610 | 10 | 14 | ribonucleoside metabolic process |
| 191 | GO:0071705 | 0.0193330 | 1.281794 | 127.926052 | 146 | 316 | nitrogen compound transport |
| 192 | GO:1902914 | 0.0200549 | 8.842991 | 2.833805 | 6 | 7 | regulation of protein polyubiquitination |
| 193 | GO:1902916 | 0.0200549 | 8.842991 | 2.833805 | 6 | 7 | positive regulation of protein polyubiquitination |
| 194 | GO:1905392 | 0.0200549 | 8.842991 | 2.833805 | 6 | 7 | plant organ morphogenesis |
| 195 | GO:0006613 | 0.0200549 | 8.842991 | 2.833805 | 6 | 7 | cotranslational protein targeting to membrane |
| 196 | GO:0006614 | 0.0200549 | 8.842991 | 2.833805 | 6 | 7 | SRP-dependent cotranslational protein targeting to membrane |
| 197 | GO:0018193 | 0.0202104 | 1.426657 | 60.319562 | 73 | 149 | peptidyl-amino acid modification |
| 198 | GO:0006913 | 0.0202974 | 1.735306 | 25.504244 | 34 | 63 | nucleocytoplasmic transport |
| 199 | GO:0030518 | 0.0222937 | 2.951265 | 7.286927 | 12 | 18 | intracellular steroid hormone receptor signaling pathway |
| 200 | GO:0008593 | 0.0222937 | 2.951265 | 7.286927 | 12 | 18 | regulation of Notch signaling pathway |
| 201 | GO:0006403 | 0.0231665 | 2.110603 | 13.764195 | 20 | 34 | RNA localization |
| 202 | GO:0006733 | 0.0231665 | 2.110603 | 13.764195 | 20 | 34 | oxidoreduction coenzyme metabolic process |
| 203 | GO:0031669 | 0.0237836 | 2.583138 | 8.906244 | 14 | 22 | cellular response to nutrient levels |
| 204 | GO:0006405 | 0.0237836 | 2.583138 | 8.906244 | 14 | 22 | RNA export from nucleus |
| 205 | GO:0045787 | 0.0237836 | 2.583138 | 8.906244 | 14 | 22 | positive regulation of cell cycle |
| 206 | GO:0006413 | 0.0241799 | 2.362441 | 10.525561 | 16 | 26 | translational initiation |
| 207 | GO:0034613 | 0.0254375 | 1.271281 | 122.258442 | 139 | 302 | cellular protein localization |
| 208 | GO:0046907 | 0.0255743 | 1.255536 | 136.427467 | 154 | 337 | intracellular transport |
| 209 | GO:0000079 | 0.0267781 | 5.159186 | 3.643464 | 7 | 9 | regulation of cyclin-dependent protein serine/threonine kinase activity |
| 210 | GO:0046128 | 0.0267781 | 5.159186 | 3.643464 | 7 | 9 | purine ribonucleoside metabolic process |
| 211 | GO:0097352 | 0.0267781 | 5.159186 | 3.643464 | 7 | 9 | autophagosome maturation |
| 212 | GO:0009225 | 0.0267781 | 5.159186 | 3.643464 | 7 | 9 | nucleotide-sugar metabolic process |
| 213 | GO:0045292 | 0.0267781 | 5.159186 | 3.643464 | 7 | 9 | mRNA cis splicing, via spliceosome |
| 214 | GO:0006749 | 0.0267781 | 5.159186 | 3.643464 | 7 | 9 | glutathione metabolic process |
| 215 | GO:1901659 | 0.0267781 | 5.159186 | 3.643464 | 7 | 9 | glycosyl compound biosynthetic process |
| 216 | GO:1990592 | 0.0268142 | Inf | 1.619317 | 4 | 4 | protein K69-linked ufmylation |
| 217 | GO:1990564 | 0.0268142 | Inf | 1.619317 | 4 | 4 | protein polyufmylation |
| 218 | GO:0048132 | 0.0268142 | Inf | 1.619317 | 4 | 4 | female germ-line stem cell asymmetric division |
| 219 | GO:0071569 | 0.0268142 | Inf | 1.619317 | 4 | 4 | protein ufmylation |
| 220 | GO:0070129 | 0.0268142 | Inf | 1.619317 | 4 | 4 | regulation of mitochondrial translation |
| 221 | GO:0010421 | 0.0268142 | Inf | 1.619317 | 4 | 4 | hydrogen peroxide-mediated programmed cell death |
| 222 | GO:0090351 | 0.0268142 | Inf | 1.619317 | 4 | 4 | seedling development |
| 223 | GO:0097468 | 0.0268142 | Inf | 1.619317 | 4 | 4 | programmed cell death in response to reactive oxygen species |
| 224 | GO:0010668 | 0.0268142 | Inf | 1.619317 | 4 | 4 | ectodermal cell differentiation |
| 225 | GO:0110116 | 0.0268142 | Inf | 1.619317 | 4 | 4 | regulation of compound eye photoreceptor cell differentiation |
| 226 | GO:0010939 | 0.0268142 | Inf | 1.619317 | 4 | 4 | regulation of necrotic cell death |
| 227 | GO:0030447 | 0.0268142 | Inf | 1.619317 | 4 | 4 | filamentous growth |
| 228 | GO:0009219 | 0.0268142 | Inf | 1.619317 | 4 | 4 | pyrimidine deoxyribonucleotide metabolic process |
| 229 | GO:0002756 | 0.0268142 | Inf | 1.619317 | 4 | 4 | MyD88-independent toll-like receptor signaling pathway |
| 230 | GO:0008334 | 0.0268142 | Inf | 1.619317 | 4 | 4 | histone mRNA metabolic process |
| 231 | GO:0006465 | 0.0268142 | Inf | 1.619317 | 4 | 4 | signal peptide processing |
| 232 | GO:0035519 | 0.0268142 | Inf | 1.619317 | 4 | 4 | protein K29-linked ubiquitination |
| 233 | GO:0006284 | 0.0268142 | Inf | 1.619317 | 4 | 4 | base-excision repair |
| 234 | GO:0044282 | 0.0276599 | 1.830278 | 19.026976 | 26 | 47 | small molecule catabolic process |
| 235 | GO:0044772 | 0.0276599 | 1.830278 | 19.026976 | 26 | 47 | mitotic cell cycle phase transition |
| 236 | GO:0006839 | 0.0291935 | 1.690499 | 24.289757 | 32 | 60 | mitochondrial transport |
| 237 | GO:0000209 | 0.0297177 | 1.866759 | 17.407659 | 24 | 43 | protein polyubiquitination |
| 238 | GO:0070727 | 0.0309441 | 1.256652 | 123.877759 | 140 | 306 | cellular macromolecule localization |
| 239 | GO:0002097 | 0.0314684 | 3.931400 | 4.453122 | 8 | 11 | tRNA wobble base modification |
| 240 | GO:0002098 | 0.0314684 | 3.931400 | 4.453122 | 8 | 11 | tRNA wobble uridine modification |
| 241 | GO:0031163 | 0.0314684 | 3.931400 | 4.453122 | 8 | 11 | metallo-sulfur cluster assembly |
| 242 | GO:0070979 | 0.0314684 | 3.931400 | 4.453122 | 8 | 11 | protein K11-linked ubiquitination |
| 243 | GO:0016226 | 0.0314684 | 3.931400 | 4.453122 | 8 | 11 | iron-sulfur cluster assembly |
| 244 | GO:0031396 | 0.0328466 | 1.938794 | 14.978683 | 21 | 37 | regulation of protein ubiquitination |
| 245 | GO:0072330 | 0.0328466 | 1.938794 | 14.978683 | 21 | 37 | monocarboxylic acid biosynthetic process |
| 246 | GO:0006401 | 0.0331593 | 1.715069 | 21.860781 | 29 | 54 | RNA catabolic process |
| 247 | GO:0071427 | 0.0346374 | 3.317618 | 5.262781 | 9 | 13 | mRNA-containing ribonucleoprotein complex export from nucleus |
| 248 | GO:0000154 | 0.0346374 | 3.317618 | 5.262781 | 9 | 13 | rRNA modification |
| 249 | GO:0070972 | 0.0346374 | 3.317618 | 5.262781 | 9 | 13 | protein localization to endoplasmic reticulum |
| 250 | GO:0006406 | 0.0346374 | 3.317618 | 5.262781 | 9 | 13 | mRNA export from nucleus |
| 251 | GO:0051169 | 0.0348084 | 1.622312 | 26.313903 | 34 | 65 | nuclear transport |
| 252 | GO:0033157 | 0.0357974 | 2.044390 | 12.549708 | 18 | 31 | regulation of intracellular protein transport |
| 253 | GO:0051604 | 0.0357974 | 2.044390 | 12.549708 | 18 | 31 | protein maturation |
| 254 | GO:0022402 | 0.0363951 | 1.314003 | 79.346538 | 92 | 196 | cell cycle process |
| 255 | GO:0000956 | 0.0366651 | 2.091397 | 11.740049 | 17 | 29 | nuclear-transcribed mRNA catabolic process |
| 256 | GO:0071456 | 0.0366863 | 2.949438 | 6.072439 | 10 | 15 | cellular response to hypoxia |
| 257 | GO:0036294 | 0.0366863 | 2.949438 | 6.072439 | 10 | 15 | cellular response to decreased oxygen levels |
| 258 | GO:0050657 | 0.0374310 | 2.146991 | 10.930390 | 16 | 27 | nucleic acid transport |
| 259 | GO:0050658 | 0.0374310 | 2.146991 | 10.930390 | 16 | 27 | RNA transport |
| 260 | GO:0032388 | 0.0374310 | 2.146991 | 10.930390 | 16 | 27 | positive regulation of intracellular transport |
| 261 | GO:0051236 | 0.0374310 | 2.146991 | 10.930390 | 16 | 27 | establishment of RNA localization |
| 262 | GO:0006888 | 0.0374310 | 2.146991 | 10.930390 | 16 | 27 | ER to Golgi vesicle-mediated transport |
| 263 | GO:0032386 | 0.0375962 | 1.746527 | 19.431805 | 26 | 48 | regulation of intracellular transport |
| 264 | GO:0090068 | 0.0379097 | 2.704059 | 6.882098 | 11 | 17 | positive regulation of cell cycle process |
| 265 | GO:0031668 | 0.0384947 | 2.295393 | 9.311073 | 14 | 23 | cellular response to extracellular stimulus |
| 266 | GO:0046394 | 0.0398556 | 1.636896 | 23.884927 | 31 | 59 | carboxylic acid biosynthetic process |
| 267 | GO:0016053 | 0.0398556 | 1.636896 | 23.884927 | 31 | 59 | organic acid biosynthetic process |
| 268 | GO:0034622 | 0.0412865 | 1.308288 | 76.917563 | 89 | 190 | cellular protein-containing complex assembly |
| 269 | GO:0055086 | 0.0425111 | 1.314163 | 73.274099 | 85 | 181 | nucleobase-containing small molecule metabolic process |
| 270 | GO:0071616 | 0.0431411 | 7.365717 | 2.428976 | 5 | 6 | acyl-CoA biosynthetic process |
| 271 | GO:0097354 | 0.0431411 | 7.365717 | 2.428976 | 5 | 6 | prenylation |
| 272 | GO:0009066 | 0.0431411 | 7.365717 | 2.428976 | 5 | 6 | aspartate family amino acid metabolic process |
| 273 | GO:0009081 | 0.0431411 | 7.365717 | 2.428976 | 5 | 6 | branched-chain amino acid metabolic process |
| 274 | GO:0035384 | 0.0431411 | 7.365717 | 2.428976 | 5 | 6 | thioester biosynthetic process |
| 275 | GO:0018342 | 0.0431411 | 7.365717 | 2.428976 | 5 | 6 | protein prenylation |
| 276 | GO:0006378 | 0.0431411 | 7.365717 | 2.428976 | 5 | 6 | mRNA polyadenylation |
| 277 | GO:0051205 | 0.0431411 | 7.365717 | 2.428976 | 5 | 6 | protein insertion into membrane |
| 278 | GO:0044774 | 0.0431411 | 7.365717 | 2.428976 | 5 | 6 | mitotic DNA integrity checkpoint |
| 279 | GO:0070585 | 0.0460141 | 1.824166 | 15.383513 | 21 | 38 | protein localization to mitochondrion |
| 280 | GO:0072655 | 0.0460141 | 1.824166 | 15.383513 | 21 | 38 | establishment of protein localization to mitochondrion |
| 281 | GO:0006626 | 0.0478263 | 1.845602 | 14.573854 | 20 | 36 | protein targeting to mitochondrion |
Module 3
GO_term_brown <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_brown.csv")
GO_term_brown %>%
kbl() %>%
kable_styling(bootstrap_options = "striped", full_width = F, position = "left") %>%
kable_paper() %>%
scroll_box(width = "800px", height = "200px")| X | GOBPID | Pvalue | OddsRatio | ExpCount | Count | Size | Term |
|---|---|---|---|---|---|---|---|
| 1 | GO:0006468 | 0.0000000 | 2.525758 | 37.2090172 | 76 | 383 | protein phosphorylation |
| 2 | GO:0016310 | 0.0000000 | 2.157007 | 44.3010753 | 80 | 456 | phosphorylation |
| 3 | GO:0036211 | 0.0000006 | 1.752425 | 84.0360309 | 125 | 865 | protein modification process |
| 4 | GO:0006464 | 0.0000006 | 1.752425 | 84.0360309 | 125 | 865 | cellular protein modification process |
| 5 | GO:0050766 | 0.0000021 | 14.169961 | 1.4572722 | 9 | 15 | positive regulation of phagocytosis |
| 6 | GO:0006793 | 0.0000021 | 1.762184 | 70.6291266 | 107 | 727 | phosphorus metabolic process |
| 7 | GO:0006796 | 0.0000027 | 1.754438 | 70.1433692 | 106 | 722 | phosphate-containing compound metabolic process |
| 8 | GO:0021549 | 0.0000030 | 8.682870 | 2.2344841 | 11 | 23 | cerebellum development |
| 9 | GO:0022037 | 0.0000030 | 8.682870 | 2.2344841 | 11 | 23 | metencephalon development |
| 10 | GO:0048026 | 0.0000062 | 15.087968 | 1.2629693 | 8 | 13 | positive regulation of mRNA splicing, via spliceosome |
| 11 | GO:0050685 | 0.0000062 | 15.087968 | 1.2629693 | 8 | 13 | positive regulation of mRNA processing |
| 12 | GO:0033120 | 0.0000062 | 15.087968 | 1.2629693 | 8 | 13 | positive regulation of RNA splicing |
| 13 | GO:0042026 | 0.0000082 | 7.439342 | 2.4287870 | 11 | 25 | protein refolding |
| 14 | GO:0061077 | 0.0000105 | 6.319417 | 2.9145444 | 12 | 30 | chaperone-mediated protein folding |
| 15 | GO:0007186 | 0.0000128 | 2.767897 | 12.6296925 | 29 | 130 | G protein-coupled receptor signaling pathway |
| 16 | GO:0030902 | 0.0000130 | 6.941931 | 2.5259385 | 11 | 26 | hindbrain development |
| 17 | GO:0048488 | 0.0000133 | 12.570677 | 1.3601207 | 8 | 14 | synaptic vesicle endocytosis |
| 18 | GO:0140238 | 0.0000133 | 12.570677 | 1.3601207 | 8 | 14 | presynaptic endocytosis |
| 19 | GO:0043412 | 0.0000154 | 1.609085 | 90.9337861 | 127 | 936 | macromolecule modification |
| 20 | GO:0061740 | 0.0000183 | 16.473425 | 1.0686663 | 7 | 11 | protein targeting to lysosome involved in chaperone-mediated autophagy |
| 21 | GO:0071211 | 0.0000183 | 16.473425 | 1.0686663 | 7 | 11 | protein targeting to vacuole involved in autophagy |
| 22 | GO:0090083 | 0.0000183 | 16.473425 | 1.0686663 | 7 | 11 | regulation of inclusion body assembly |
| 23 | GO:0090084 | 0.0000183 | 16.473425 | 1.0686663 | 7 | 11 | negative regulation of inclusion body assembly |
| 24 | GO:0061462 | 0.0000183 | 16.473425 | 1.0686663 | 7 | 11 | protein localization to lysosome |
| 25 | GO:0006622 | 0.0000183 | 16.473425 | 1.0686663 | 7 | 11 | protein targeting to lysosome |
| 26 | GO:0034605 | 0.0000244 | 7.270373 | 2.2344841 | 10 | 23 | cellular response to heat |
| 27 | GO:0010662 | 0.0000261 | 10.772612 | 1.4572722 | 8 | 15 | regulation of striated muscle cell apoptotic process |
| 28 | GO:0010664 | 0.0000261 | 10.772612 | 1.4572722 | 8 | 15 | negative regulation of striated muscle cell apoptotic process |
| 29 | GO:0010665 | 0.0000261 | 10.772612 | 1.4572722 | 8 | 15 | regulation of cardiac muscle cell apoptotic process |
| 30 | GO:0010667 | 0.0000261 | 10.772612 | 1.4572722 | 8 | 15 | negative regulation of cardiac muscle cell apoptotic process |
| 31 | GO:0010656 | 0.0000261 | 10.772612 | 1.4572722 | 8 | 15 | negative regulation of muscle cell apoptotic process |
| 32 | GO:0010658 | 0.0000261 | 10.772612 | 1.4572722 | 8 | 15 | striated muscle cell apoptotic process |
| 33 | GO:0010659 | 0.0000261 | 10.772612 | 1.4572722 | 8 | 15 | cardiac muscle cell apoptotic process |
| 34 | GO:0019538 | 0.0000382 | 1.494413 | 136.9835880 | 176 | 1410 | protein metabolic process |
| 35 | GO:0044849 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | estrous cycle |
| 36 | GO:0061741 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | chaperone-mediated protein transport involved in chaperone-mediated autophagy |
| 37 | GO:0061738 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | late endosomal microautophagy |
| 38 | GO:1990832 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | slow axonal transport |
| 39 | GO:1990834 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | response to odorant |
| 40 | GO:0061684 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | chaperone-mediated autophagy |
| 41 | GO:1904764 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | chaperone-mediated autophagy translocation complex disassembly |
| 42 | GO:0010045 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | response to nickel cation |
| 43 | GO:1904592 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | positive regulation of protein refolding |
| 44 | GO:0070841 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | inclusion body assembly |
| 45 | GO:0001913 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | T cell mediated cytotoxicity |
| 46 | GO:0001914 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | regulation of T cell mediated cytotoxicity |
| 47 | GO:0001916 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | positive regulation of T cell mediated cytotoxicity |
| 48 | GO:0097212 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | lysosomal membrane organization |
| 49 | GO:0097213 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | regulation of lysosomal membrane permeability |
| 50 | GO:0097214 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | positive regulation of lysosomal membrane permeability |
| 51 | GO:0072318 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | clathrin coat disassembly |
| 52 | GO:0072319 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | vesicle uncoating |
| 53 | GO:0002456 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | T cell mediated immunity |
| 54 | GO:1903334 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | positive regulation of protein folding |
| 55 | GO:0002711 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | positive regulation of T cell mediated immunity |
| 56 | GO:0002709 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | regulation of T cell mediated immunity |
| 57 | GO:0016191 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | synaptic vesicle uncoating |
| 58 | GO:0006623 | 0.0000403 | 13.175984 | 1.1658178 | 7 | 12 | protein targeting to vacuole |
| 59 | GO:0010660 | 0.0000478 | 9.424063 | 1.5544237 | 8 | 16 | regulation of muscle cell apoptotic process |
| 60 | GO:0010657 | 0.0000478 | 9.424063 | 1.5544237 | 8 | 16 | muscle cell apoptotic process |
| 61 | GO:0045807 | 0.0000583 | 6.298350 | 2.4287870 | 10 | 25 | positive regulation of endocytosis |
| 62 | GO:0050764 | 0.0000726 | 7.076087 | 2.0401811 | 9 | 21 | regulation of phagocytosis |
| 63 | GO:0006458 | 0.0000726 | 7.076087 | 2.0401811 | 9 | 21 | ‘de novo’ protein folding |
| 64 | GO:0009408 | 0.0000790 | 3.850541 | 5.0518770 | 15 | 52 | response to heat |
| 65 | GO:1905710 | 0.0000800 | 10.977690 | 1.2629693 | 7 | 13 | positive regulation of membrane permeability |
| 66 | GO:0071276 | 0.0000800 | 10.977690 | 1.2629693 | 7 | 13 | cellular response to cadmium ion |
| 67 | GO:0001912 | 0.0000800 | 10.977690 | 1.2629693 | 7 | 13 | positive regulation of leukocyte mediated cytotoxicity |
| 68 | GO:0002460 | 0.0000800 | 10.977690 | 1.2629693 | 7 | 13 | adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains |
| 69 | GO:0002250 | 0.0000800 | 10.977690 | 1.2629693 | 7 | 13 | adaptive immune response |
| 70 | GO:0002821 | 0.0000800 | 10.977690 | 1.2629693 | 7 | 13 | positive regulation of adaptive immune response |
| 71 | GO:0002822 | 0.0000800 | 10.977690 | 1.2629693 | 7 | 13 | regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains |
| 72 | GO:0002824 | 0.0000800 | 10.977690 | 1.2629693 | 7 | 13 | positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains |
| 73 | GO:0002819 | 0.0000800 | 10.977690 | 1.2629693 | 7 | 13 | regulation of adaptive immune response |
| 74 | GO:0061083 | 0.0000800 | 10.977690 | 1.2629693 | 7 | 13 | regulation of protein refolding |
| 75 | GO:0036465 | 0.0000827 | 8.375192 | 1.6515752 | 8 | 17 | synaptic vesicle recycling |
| 76 | GO:1903313 | 0.0000827 | 8.375192 | 1.6515752 | 8 | 17 | positive regulation of mRNA metabolic process |
| 77 | GO:1903332 | 0.0000827 | 8.375192 | 1.6515752 | 8 | 17 | regulation of protein folding |
| 78 | GO:0035821 | 0.0000827 | 8.375192 | 1.6515752 | 8 | 17 | modification of morphology or physiology of other organism |
| 79 | GO:0051817 | 0.0000827 | 8.375192 | 1.6515752 | 8 | 17 | modification of morphology or physiology of other organism involved in symbiotic interaction |
| 80 | GO:0051261 | 0.0000867 | 5.903465 | 2.5259385 | 10 | 26 | protein depolymerization |
| 81 | GO:0002443 | 0.0001258 | 5.555038 | 2.6230900 | 10 | 27 | leukocyte mediated immunity |
| 82 | GO:0032570 | 0.0001363 | 7.536095 | 1.7487267 | 8 | 18 | response to progesterone |
| 83 | GO:1903202 | 0.0001363 | 7.536095 | 1.7487267 | 8 | 18 | negative regulation of oxidative stress-induced cell death |
| 84 | GO:0044829 | 0.0001466 | 9.407480 | 1.3601207 | 7 | 14 | positive regulation by host of viral genome replication |
| 85 | GO:0061635 | 0.0001466 | 9.407480 | 1.3601207 | 7 | 14 | regulation of protein complex stability |
| 86 | GO:2001039 | 0.0001466 | 9.407480 | 1.3601207 | 7 | 14 | negative regulation of cellular response to drug |
| 87 | GO:0001910 | 0.0001466 | 9.407480 | 1.3601207 | 7 | 14 | regulation of leukocyte mediated cytotoxicity |
| 88 | GO:0001909 | 0.0001466 | 9.407480 | 1.3601207 | 7 | 14 | leukocyte mediated cytotoxicity |
| 89 | GO:0031343 | 0.0001466 | 9.407480 | 1.3601207 | 7 | 14 | positive regulation of cell killing |
| 90 | GO:0007608 | 0.0001466 | 9.407480 | 1.3601207 | 7 | 14 | sensory perception of smell |
| 91 | GO:1901032 | 0.0001466 | 9.407480 | 1.3601207 | 7 | 14 | negative regulation of response to reactive oxygen species |
| 92 | GO:0002705 | 0.0001466 | 9.407480 | 1.3601207 | 7 | 14 | positive regulation of leukocyte mediated immunity |
| 93 | GO:0002708 | 0.0001466 | 9.407480 | 1.3601207 | 7 | 14 | positive regulation of lymphocyte mediated immunity |
| 94 | GO:1903206 | 0.0001466 | 9.407480 | 1.3601207 | 7 | 14 | negative regulation of hydrogen peroxide-induced cell death |
| 95 | GO:0032879 | 0.0001844 | 1.948133 | 25.5508395 | 44 | 263 | regulation of localization |
| 96 | GO:0048024 | 0.0002157 | 6.849561 | 1.8458781 | 8 | 19 | regulation of mRNA splicing, via spliceosome |
| 97 | GO:1903201 | 0.0002157 | 6.849561 | 1.8458781 | 8 | 19 | regulation of oxidative stress-induced cell death |
| 98 | GO:0032355 | 0.0002157 | 6.849561 | 1.8458781 | 8 | 19 | response to estradiol |
| 99 | GO:0009266 | 0.0002458 | 3.388571 | 5.5376344 | 15 | 57 | response to temperature stimulus |
| 100 | GO:0044827 | 0.0002520 | 8.229823 | 1.4572722 | 7 | 15 | modulation by host of viral genome replication |
| 101 | GO:0042698 | 0.0002520 | 8.229823 | 1.4572722 | 7 | 15 | ovulation cycle |
| 102 | GO:2001024 | 0.0002520 | 8.229823 | 1.4572722 | 7 | 15 | negative regulation of response to drug |
| 103 | GO:2001038 | 0.0002520 | 8.229823 | 1.4572722 | 7 | 15 | regulation of cellular response to drug |
| 104 | GO:0001906 | 0.0002520 | 8.229823 | 1.4572722 | 7 | 15 | cell killing |
| 105 | GO:0031341 | 0.0002520 | 8.229823 | 1.4572722 | 7 | 15 | regulation of cell killing |
| 106 | GO:0090559 | 0.0002520 | 8.229823 | 1.4572722 | 7 | 15 | regulation of membrane permeability |
| 107 | GO:0002449 | 0.0002520 | 8.229823 | 1.4572722 | 7 | 15 | lymphocyte mediated immunity |
| 108 | GO:0002703 | 0.0002520 | 8.229823 | 1.4572722 | 7 | 15 | regulation of leukocyte mediated immunity |
| 109 | GO:0002706 | 0.0002520 | 8.229823 | 1.4572722 | 7 | 15 | regulation of lymphocyte mediated immunity |
| 110 | GO:0045070 | 0.0002520 | 8.229823 | 1.4572722 | 7 | 15 | positive regulation of viral genome replication |
| 111 | GO:1903205 | 0.0002520 | 8.229823 | 1.4572722 | 7 | 15 | regulation of hydrogen peroxide-induced cell death |
| 112 | GO:0072665 | 0.0002520 | 8.229823 | 1.4572722 | 7 | 15 | protein localization to vacuole |
| 113 | GO:0072666 | 0.0002520 | 8.229823 | 1.4572722 | 7 | 15 | establishment of protein localization to vacuole |
| 114 | GO:0044794 | 0.0002520 | 8.229823 | 1.4572722 | 7 | 15 | positive regulation by host of viral process |
| 115 | GO:0044788 | 0.0002520 | 8.229823 | 1.4572722 | 7 | 15 | modulation by host of viral process |
| 116 | GO:0050684 | 0.0003292 | 6.277449 | 1.9430296 | 8 | 20 | regulation of mRNA processing |
| 117 | GO:1900408 | 0.0003292 | 6.277449 | 1.9430296 | 8 | 20 | negative regulation of cellular response to oxidative stress |
| 118 | GO:0006457 | 0.0003505 | 2.683170 | 8.8407848 | 20 | 91 | protein folding |
| 119 | GO:0034504 | 0.0003524 | 3.913347 | 3.9832107 | 12 | 41 | protein localization to nucleus |
| 120 | GO:0042542 | 0.0003537 | 5.302619 | 2.4287870 | 9 | 25 | response to hydrogen peroxide |
| 121 | GO:0090169 | 0.0003707 | 15.630719 | 0.7772118 | 5 | 8 | regulation of spindle assembly |
| 122 | GO:1901673 | 0.0003707 | 15.630719 | 0.7772118 | 5 | 8 | regulation of mitotic spindle assembly |
| 123 | GO:0006508 | 0.0004062 | 1.725352 | 36.8204112 | 57 | 379 | proteolysis |
| 124 | GO:0036474 | 0.0004108 | 7.313867 | 1.5544237 | 7 | 16 | cell death in response to hydrogen peroxide |
| 125 | GO:0072321 | 0.0004108 | 7.313867 | 1.5544237 | 7 | 16 | chaperone-mediated protein transport |
| 126 | GO:1901031 | 0.0004108 | 7.313867 | 1.5544237 | 7 | 16 | regulation of response to reactive oxygen species |
| 127 | GO:1903902 | 0.0004108 | 7.313867 | 1.5544237 | 7 | 16 | positive regulation of viral life cycle |
| 128 | GO:0051702 | 0.0004108 | 7.313867 | 1.5544237 | 7 | 16 | interaction with symbiont |
| 129 | GO:0051851 | 0.0004108 | 7.313867 | 1.5544237 | 7 | 16 | modification by host of symbiont morphology or physiology |
| 130 | GO:1902904 | 0.0004625 | 4.493164 | 3.0116959 | 10 | 31 | negative regulation of supramolecular fiber organization |
| 131 | GO:0099003 | 0.0004625 | 4.493164 | 3.0116959 | 10 | 31 | vesicle-mediated transport in synapse |
| 132 | GO:0070301 | 0.0004871 | 5.793355 | 2.0401811 | 8 | 21 | cellular response to hydrogen peroxide |
| 133 | GO:1902883 | 0.0004871 | 5.793355 | 2.0401811 | 8 | 21 | negative regulation of response to oxidative stress |
| 134 | GO:0007606 | 0.0004871 | 5.793355 | 2.0401811 | 8 | 21 | sensory perception of chemical stimulus |
| 135 | GO:0008088 | 0.0004871 | 5.793355 | 2.0401811 | 8 | 21 | axo-dendritic transport |
| 136 | GO:0030100 | 0.0005340 | 3.995726 | 3.5946048 | 11 | 37 | regulation of endocytosis |
| 137 | GO:0099504 | 0.0006153 | 4.288029 | 3.1088474 | 10 | 32 | synaptic vesicle cycle |
| 138 | GO:0051085 | 0.0006405 | 6.581102 | 1.6515752 | 7 | 17 | chaperone cofactor-dependent protein refolding |
| 139 | GO:1900407 | 0.0007013 | 5.378417 | 2.1373326 | 8 | 22 | regulation of cellular response to oxidative stress |
| 140 | GO:0006814 | 0.0007175 | 3.544235 | 4.2746652 | 12 | 44 | sodium ion transport |
| 141 | GO:0060236 | 0.0007677 | 11.720588 | 0.8743633 | 5 | 9 | regulation of mitotic spindle organization |
| 142 | GO:0090063 | 0.0007677 | 11.720588 | 0.8743633 | 5 | 9 | positive regulation of microtubule nucleation |
| 143 | GO:0070868 | 0.0007677 | 11.720588 | 0.8743633 | 5 | 9 | heterochromatin organization involved in chromatin silencing |
| 144 | GO:0046685 | 0.0007677 | 11.720588 | 0.8743633 | 5 | 9 | response to arsenic-containing substance |
| 145 | GO:0090224 | 0.0007677 | 11.720588 | 0.8743633 | 5 | 9 | regulation of spindle organization |
| 146 | GO:0097549 | 0.0007677 | 11.720588 | 0.8743633 | 5 | 9 | chromatin organization involved in negative regulation of transcription |
| 147 | GO:0010968 | 0.0007677 | 11.720588 | 0.8743633 | 5 | 9 | regulation of microtubule nucleation |
| 148 | GO:0034401 | 0.0007677 | 11.720588 | 0.8743633 | 5 | 9 | chromatin organization involved in regulation of transcription |
| 149 | GO:1901564 | 0.0008470 | 1.358999 | 169.3350311 | 202 | 1743 | organonitrogen compound metabolic process |
| 150 | GO:0030900 | 0.0008748 | 3.708759 | 3.7889078 | 11 | 39 | forebrain development |
| 151 | GO:0061588 | 0.0009121 | Inf | 0.2914544 | 3 | 3 | calcium activated phospholipid scrambling |
| 152 | GO:0007040 | 0.0009613 | 5.981568 | 1.7487267 | 7 | 18 | lysosome organization |
| 153 | GO:0080171 | 0.0009613 | 5.981568 | 1.7487267 | 7 | 18 | lytic vacuole organization |
| 154 | GO:0051084 | 0.0009613 | 5.981568 | 1.7487267 | 7 | 18 | ‘de novo’ posttranslational protein folding |
| 155 | GO:0036473 | 0.0009851 | 5.018803 | 2.2344841 | 8 | 23 | cell death in response to oxidative stress |
| 156 | GO:0043484 | 0.0009851 | 5.018803 | 2.2344841 | 8 | 23 | regulation of RNA splicing |
| 157 | GO:0045862 | 0.0010464 | 3.929043 | 3.3031503 | 10 | 34 | positive regulation of proteolysis |
| 158 | GO:0048260 | 0.0011263 | 18.724070 | 0.5829089 | 4 | 6 | positive regulation of receptor-mediated endocytosis |
| 159 | GO:0018022 | 0.0012170 | 4.238537 | 2.8173929 | 9 | 29 | peptidyl-lysine methylation |
| 160 | GO:0010970 | 0.0013402 | 3.771089 | 3.4003018 | 10 | 35 | transport along microtubule |
| 161 | GO:1903311 | 0.0013402 | 3.771089 | 3.4003018 | 10 | 35 | regulation of mRNA metabolic process |
| 162 | GO:0099111 | 0.0013402 | 3.771089 | 3.4003018 | 10 | 35 | microtubule-based transport |
| 163 | GO:0034614 | 0.0013540 | 4.704142 | 2.3316355 | 8 | 24 | cellular response to reactive oxygen species |
| 164 | GO:0046777 | 0.0013963 | 5.481955 | 1.8458781 | 7 | 19 | protein autophosphorylation |
| 165 | GO:0046686 | 0.0013963 | 5.481955 | 1.8458781 | 7 | 19 | response to cadmium ion |
| 166 | GO:0014823 | 0.0013963 | 5.481955 | 1.8458781 | 7 | 19 | response to activity |
| 167 | GO:0045069 | 0.0013963 | 5.481955 | 1.8458781 | 7 | 19 | regulation of viral genome replication |
| 168 | GO:0002699 | 0.0013963 | 5.481955 | 1.8458781 | 7 | 19 | positive regulation of immune effector process |
| 169 | GO:0045471 | 0.0013963 | 5.481955 | 1.8458781 | 7 | 19 | response to ethanol |
| 170 | GO:0007413 | 0.0014134 | 9.374510 | 0.9715148 | 5 | 10 | axonal fasciculation |
| 171 | GO:0070828 | 0.0014134 | 9.374510 | 0.9715148 | 5 | 10 | heterochromatin organization |
| 172 | GO:0106030 | 0.0014134 | 9.374510 | 0.9715148 | 5 | 10 | neuron projection fasciculation |
| 173 | GO:0032781 | 0.0014134 | 9.374510 | 0.9715148 | 5 | 10 | positive regulation of ATPase activity |
| 174 | GO:0030705 | 0.0016977 | 3.625286 | 3.4974533 | 10 | 36 | cytoskeleton-dependent intracellular transport |
| 175 | GO:0007018 | 0.0018092 | 2.679057 | 6.6063007 | 15 | 68 | microtubule-based movement |
| 176 | GO:1902882 | 0.0018248 | 4.426500 | 2.4287870 | 8 | 25 | regulation of response to oxidative stress |
| 177 | GO:0097237 | 0.0018248 | 4.426500 | 2.4287870 | 8 | 25 | cellular response to toxic substance |
| 178 | GO:0043462 | 0.0019012 | 6.256712 | 1.4572722 | 6 | 15 | regulation of ATPase activity |
| 179 | GO:2001023 | 0.0019708 | 5.059207 | 1.9430296 | 7 | 20 | regulation of response to drug |
| 180 | GO:0048524 | 0.0019708 | 5.059207 | 1.9430296 | 7 | 20 | positive regulation of viral process |
| 181 | GO:0019079 | 0.0019708 | 5.059207 | 1.9430296 | 7 | 20 | viral genome replication |
| 182 | GO:0000302 | 0.0020537 | 3.851599 | 3.0116959 | 9 | 31 | response to reactive oxygen species |
| 183 | GO:0043624 | 0.0021287 | 3.490282 | 3.5946048 | 10 | 37 | cellular protein complex disassembly |
| 184 | GO:0006897 | 0.0021616 | 2.525584 | 7.3835125 | 16 | 76 | endocytosis |
| 185 | GO:0006812 | 0.0022718 | 1.819278 | 20.6932654 | 34 | 213 | cation transport |
| 186 | GO:0032880 | 0.0023978 | 2.282386 | 9.5208451 | 19 | 98 | regulation of protein localization |
| 187 | GO:0048511 | 0.0024056 | 2.980852 | 4.8575740 | 12 | 50 | rhythmic process |
| 188 | GO:0071236 | 0.0024158 | 4.179706 | 2.5259385 | 8 | 26 | cellular response to antibiotic |
| 189 | GO:0031099 | 0.0024158 | 4.179706 | 2.5259385 | 8 | 26 | regeneration |
| 190 | GO:1903842 | 0.0024267 | 12.480104 | 0.6800604 | 4 | 7 | response to arsenite ion |
| 191 | GO:0051170 | 0.0026165 | 3.683365 | 3.1088474 | 9 | 32 | import into nucleus |
| 192 | GO:0016032 | 0.0026436 | 3.364922 | 3.6917563 | 10 | 38 | viral process |
| 193 | GO:0071248 | 0.0027127 | 4.696850 | 2.0401811 | 7 | 21 | cellular response to metal ion |
| 194 | GO:0046785 | 0.0027127 | 4.696850 | 2.0401811 | 7 | 21 | microtubule polymerization |
| 195 | GO:0008037 | 0.0027127 | 4.696850 | 2.0401811 | 7 | 21 | cell recognition |
| 196 | GO:1903747 | 0.0027127 | 4.696850 | 2.0401811 | 7 | 21 | regulation of establishment of protein localization to mitochondrion |
| 197 | GO:0007417 | 0.0027888 | 2.063967 | 12.5325410 | 23 | 129 | central nervous system development |
| 198 | GO:0051225 | 0.0027955 | 5.629862 | 1.5544237 | 6 | 16 | spindle assembly |
| 199 | GO:0002252 | 0.0034172 | 2.830616 | 5.0518770 | 12 | 52 | immune effector process |
| 200 | GO:0051172 | 0.0035614 | 1.744683 | 22.0533862 | 35 | 227 | negative regulation of nitrogen compound metabolic process |
| 201 | GO:0000082 | 0.0036513 | 4.382808 | 2.1373326 | 7 | 22 | G1/S transition of mitotic cell cycle |
| 202 | GO:0071241 | 0.0036513 | 4.382808 | 2.1373326 | 7 | 22 | cellular response to inorganic substance |
| 203 | GO:1903900 | 0.0036513 | 4.382808 | 2.1373326 | 7 | 22 | regulation of viral life cycle |
| 204 | GO:0050776 | 0.0037308 | 2.543989 | 6.4119977 | 14 | 66 | regulation of immune response |
| 205 | GO:0090307 | 0.0037665 | 6.693277 | 1.1658178 | 5 | 12 | mitotic spindle assembly |
| 206 | GO:0009583 | 0.0037665 | 6.693277 | 1.1658178 | 5 | 12 | detection of light stimulus |
| 207 | GO:1900034 | 0.0037665 | 6.693277 | 1.1658178 | 5 | 12 | regulation of cellular response to heat |
| 208 | GO:0042246 | 0.0039710 | 5.116985 | 1.6515752 | 6 | 17 | tissue regeneration |
| 209 | GO:0031110 | 0.0039710 | 5.116985 | 1.6515752 | 6 | 17 | regulation of microtubule polymerization or depolymerization |
| 210 | GO:2001234 | 0.0040387 | 3.760158 | 2.7202415 | 8 | 28 | negative regulation of apoptotic signaling pathway |
| 211 | GO:0019058 | 0.0040387 | 3.760158 | 2.7202415 | 8 | 28 | viral life cycle |
| 212 | GO:0006606 | 0.0040387 | 3.760158 | 2.7202415 | 8 | 28 | protein import into nucleus |
| 213 | GO:0035690 | 0.0041044 | 3.387273 | 3.3031503 | 9 | 34 | cellular response to drug |
| 214 | GO:0043066 | 0.0042495 | 2.328842 | 7.8692699 | 16 | 81 | negative regulation of apoptotic process |
| 215 | GO:0060322 | 0.0042946 | 2.144249 | 10.0066025 | 19 | 103 | head development |
| 216 | GO:0009628 | 0.0044260 | 1.840232 | 16.8072062 | 28 | 173 | response to abiotic stimulus |
| 217 | GO:0009584 | 0.0044826 | 9.358121 | 0.7772118 | 4 | 8 | detection of visible light |
| 218 | GO:0046677 | 0.0048066 | 3.037368 | 3.9832107 | 10 | 41 | response to antibiotic |
| 219 | GO:0007041 | 0.0048178 | 4.108022 | 2.2344841 | 7 | 23 | lysosomal transport |
| 220 | GO:0031109 | 0.0048178 | 4.108022 | 2.2344841 | 7 | 23 | microtubule polymerization or depolymerization |
| 221 | GO:0002697 | 0.0048178 | 4.108022 | 2.2344841 | 7 | 23 | regulation of immune effector process |
| 222 | GO:0006909 | 0.0050612 | 3.256309 | 3.4003018 | 9 | 35 | phagocytosis |
| 223 | GO:1901654 | 0.0051137 | 3.580351 | 2.8173929 | 8 | 29 | response to ketone |
| 224 | GO:0098657 | 0.0054517 | 2.258367 | 8.0635729 | 16 | 83 | import into cell |
| 225 | GO:0006811 | 0.0055479 | 1.559118 | 33.4201094 | 48 | 344 | ion transport |
| 226 | GO:0007020 | 0.0056379 | 5.855392 | 1.2629693 | 5 | 13 | microtubule nucleation |
| 227 | GO:0031112 | 0.0056379 | 5.855392 | 1.2629693 | 5 | 13 | positive regulation of microtubule polymerization or depolymerization |
| 228 | GO:0031116 | 0.0056379 | 5.855392 | 1.2629693 | 5 | 13 | positive regulation of microtubule polymerization |
| 229 | GO:0030162 | 0.0056805 | 2.403702 | 6.7034522 | 14 | 69 | regulation of proteolysis |
| 230 | GO:0001822 | 0.0061824 | 3.135046 | 3.4974533 | 9 | 36 | kidney development |
| 231 | GO:0034599 | 0.0061824 | 3.135046 | 3.4974533 | 9 | 36 | cellular response to oxidative stress |
| 232 | GO:0044843 | 0.0062441 | 3.865563 | 2.3316355 | 7 | 24 | cell cycle G1/S phase transition |
| 233 | GO:0060627 | 0.0064614 | 2.571119 | 5.4404829 | 12 | 56 | regulation of vesicle-mediated transport |
| 234 | GO:0032502 | 0.0064862 | 1.377911 | 71.5034899 | 91 | 736 | developmental process |
| 235 | GO:0031324 | 0.0066964 | 1.663298 | 22.9277495 | 35 | 236 | negative regulation of cellular metabolic process |
| 236 | GO:0051049 | 0.0066966 | 1.817936 | 15.7385399 | 26 | 162 | regulation of transport |
| 237 | GO:0055085 | 0.0068746 | 1.469961 | 44.1067723 | 60 | 454 | transmembrane transport |
| 238 | GO:0043069 | 0.0069164 | 2.191978 | 8.2578759 | 16 | 85 | negative regulation of programmed cell death |
| 239 | GO:0007420 | 0.0069894 | 2.077637 | 9.7151481 | 18 | 100 | brain development |
| 240 | GO:1902850 | 0.0073586 | 4.327943 | 1.8458781 | 6 | 19 | microtubule cytoskeleton organization involved in mitosis |
| 241 | GO:1903214 | 0.0073586 | 4.327943 | 1.8458781 | 6 | 19 | regulation of protein targeting to mitochondrion |
| 242 | GO:1903749 | 0.0073586 | 4.327943 | 1.8458781 | 6 | 19 | positive regulation of establishment of protein localization to mitochondrion |
| 243 | GO:1903955 | 0.0073586 | 4.327943 | 1.8458781 | 6 | 19 | positive regulation of protein targeting to mitochondrion |
| 244 | GO:0048568 | 0.0073838 | 2.318381 | 6.8977551 | 14 | 71 | embryonic organ development |
| 245 | GO:0031400 | 0.0073838 | 2.318381 | 6.8977551 | 14 | 71 | negative regulation of protein modification process |
| 246 | GO:0060760 | 0.0074545 | 7.484932 | 0.8743633 | 4 | 9 | positive regulation of response to cytokine stimulus |
| 247 | GO:0060759 | 0.0074545 | 7.484932 | 0.8743633 | 4 | 9 | regulation of response to cytokine stimulus |
| 248 | GO:0048259 | 0.0074545 | 7.484932 | 0.8743633 | 4 | 9 | regulation of receptor-mediated endocytosis |
| 249 | GO:0007339 | 0.0074545 | 7.484932 | 0.8743633 | 4 | 9 | binding of sperm to zona pellucida |
| 250 | GO:0001961 | 0.0074545 | 7.484932 | 0.8743633 | 4 | 9 | positive regulation of cytokine-mediated signaling pathway |
| 251 | GO:0001959 | 0.0074545 | 7.484932 | 0.8743633 | 4 | 9 | regulation of cytokine-mediated signaling pathway |
| 252 | GO:0035036 | 0.0074545 | 7.484932 | 0.8743633 | 4 | 9 | sperm-egg recognition |
| 253 | GO:0009988 | 0.0074545 | 7.484932 | 0.8743633 | 4 | 9 | cell-cell recognition |
| 254 | GO:0048513 | 0.0076372 | 1.501865 | 37.4033201 | 52 | 385 | animal organ development |
| 255 | GO:0007275 | 0.0076828 | 1.397620 | 60.2339181 | 78 | 620 | multicellular organism development |
| 256 | GO:0032677 | 0.0078502 | 14.015625 | 0.4857574 | 3 | 5 | regulation of interleukin-8 production |
| 257 | GO:0032637 | 0.0078502 | 14.015625 | 0.4857574 | 3 | 5 | interleukin-8 production |
| 258 | GO:1902380 | 0.0078502 | 14.015625 | 0.4857574 | 3 | 5 | positive regulation of endoribonuclease activity |
| 259 | GO:0060700 | 0.0078502 | 14.015625 | 0.4857574 | 3 | 5 | regulation of ribonuclease activity |
| 260 | GO:0070370 | 0.0078502 | 14.015625 | 0.4857574 | 3 | 5 | cellular heat acclimation |
| 261 | GO:0060699 | 0.0078502 | 14.015625 | 0.4857574 | 3 | 5 | regulation of endoribonuclease activity |
| 262 | GO:0097035 | 0.0078502 | 14.015625 | 0.4857574 | 3 | 5 | regulation of membrane lipid distribution |
| 263 | GO:0017121 | 0.0078502 | 14.015625 | 0.4857574 | 3 | 5 | phospholipid scrambling |
| 264 | GO:0097201 | 0.0078502 | 14.015625 | 0.4857574 | 3 | 5 | negative regulation of transcription from RNA polymerase II promoter in response to stress |
| 265 | GO:0032757 | 0.0078502 | 14.015625 | 0.4857574 | 3 | 5 | positive regulation of interleukin-8 production |
| 266 | GO:0007519 | 0.0079042 | 3.267644 | 3.0116959 | 8 | 31 | skeletal muscle tissue development |
| 267 | GO:0050792 | 0.0079627 | 3.650044 | 2.4287870 | 7 | 25 | regulation of viral process |
| 268 | GO:0051783 | 0.0079627 | 3.650044 | 2.4287870 | 7 | 25 | regulation of nuclear division |
| 269 | GO:0007052 | 0.0080804 | 5.203704 | 1.3601207 | 5 | 14 | mitotic spindle organization |
| 270 | GO:0001700 | 0.0080804 | 5.203704 | 1.3601207 | 5 | 14 | embryonic development via the syncytial blastoderm |
| 271 | GO:0031113 | 0.0080804 | 5.203704 | 1.3601207 | 5 | 14 | regulation of microtubule polymerization |
| 272 | GO:0016246 | 0.0080804 | 5.203704 | 1.3601207 | 5 | 14 | RNA interference |
| 273 | GO:0048731 | 0.0082078 | 1.427018 | 50.6159215 | 67 | 521 | system development |
| 274 | GO:0048856 | 0.0085855 | 1.377038 | 64.9943407 | 83 | 669 | anatomical structure development |
| 275 | GO:0032269 | 0.0086032 | 2.027307 | 9.9094510 | 18 | 102 | negative regulation of cellular protein metabolic process |
| 276 | GO:0032501 | 0.0087486 | 1.358400 | 72.2807018 | 91 | 744 | multicellular organismal process |
| 277 | GO:0045934 | 0.0093500 | 1.833385 | 13.7955103 | 23 | 142 | negative regulation of nucleobase-containing compound metabolic process |
| 278 | GO:0042493 | 0.0095156 | 2.003030 | 10.0066025 | 18 | 103 | response to drug |
| 279 | GO:0044403 | 0.0096109 | 2.687977 | 4.3718166 | 10 | 45 | symbiont process |
| 280 | GO:0009566 | 0.0096677 | 4.017962 | 1.9430296 | 6 | 20 | fertilization |
| 281 | GO:1903533 | 0.0096677 | 4.017962 | 1.9430296 | 6 | 20 | regulation of protein targeting |
| 282 | GO:0032886 | 0.0100063 | 3.457211 | 2.5259385 | 7 | 26 | regulation of microtubule-based process |
| 283 | GO:0044743 | 0.0100063 | 3.457211 | 2.5259385 | 7 | 26 | protein transmembrane import into intracellular organelle |
| 284 | GO:0007338 | 0.0111699 | 4.682353 | 1.4572722 | 5 | 15 | single fertilization |
| 285 | GO:0001895 | 0.0111699 | 4.682353 | 1.4572722 | 5 | 15 | retina homeostasis |
| 286 | GO:0010921 | 0.0111699 | 4.682353 | 1.4572722 | 5 | 15 | regulation of phosphatase activity |
| 287 | GO:0019221 | 0.0111699 | 4.682353 | 1.4572722 | 5 | 15 | cytokine-mediated signaling pathway |
| 288 | GO:0009605 | 0.0111809 | 1.620567 | 22.0533862 | 33 | 227 | response to external stimulus |
| 289 | GO:0008213 | 0.0112465 | 2.612761 | 4.4689681 | 10 | 46 | protein alkylation |
| 290 | GO:0006479 | 0.0112465 | 2.612761 | 4.4689681 | 10 | 46 | protein methylation |
| 291 | GO:0009636 | 0.0114187 | 2.465231 | 5.1490285 | 11 | 53 | response to toxic substance |
| 292 | GO:2001237 | 0.0114818 | 6.236138 | 0.9715148 | 4 | 10 | negative regulation of extrinsic apoptotic signaling pathway |
| 293 | GO:0046688 | 0.0114818 | 6.236138 | 0.9715148 | 4 | 10 | response to copper ion |
| 294 | GO:0021695 | 0.0114818 | 6.236138 | 0.9715148 | 4 | 10 | cerebellar cortex development |
| 295 | GO:0021680 | 0.0114818 | 6.236138 | 0.9715148 | 4 | 10 | cerebellar Purkinje cell layer development |
| 296 | GO:0043666 | 0.0114818 | 6.236138 | 0.9715148 | 4 | 10 | regulation of phosphoprotein phosphatase activity |
| 297 | GO:1902115 | 0.0117057 | 3.004970 | 3.2059989 | 8 | 33 | regulation of organelle assembly |
| 298 | GO:0060538 | 0.0117057 | 3.004970 | 3.2059989 | 8 | 33 | skeletal muscle organ development |
| 299 | GO:0051129 | 0.0119870 | 2.041705 | 8.7436333 | 16 | 90 | negative regulation of cellular component organization |
| 300 | GO:0007088 | 0.0124497 | 3.749312 | 2.0401811 | 6 | 21 | regulation of mitotic nuclear division |
| 301 | GO:0050790 | 0.0124927 | 1.660717 | 18.9445388 | 29 | 195 | regulation of catalytic activity |
| 302 | GO:0072001 | 0.0126644 | 2.728229 | 3.8860592 | 9 | 40 | renal system development |
| 303 | GO:0031647 | 0.0126644 | 2.728229 | 3.8860592 | 9 | 40 | regulation of protein stability |
| 304 | GO:0002682 | 0.0127252 | 1.933510 | 10.2980570 | 18 | 106 | regulation of immune system process |
| 305 | GO:0044267 | 0.0130139 | 1.276784 | 115.2216563 | 136 | 1186 | cellular protein metabolic process |
| 306 | GO:0044419 | 0.0130846 | 2.541611 | 4.5661196 | 10 | 47 | interspecies interaction between organisms |
| 307 | GO:0080135 | 0.0132848 | 2.014055 | 8.8407848 | 16 | 91 | regulation of cellular response to stress |
| 308 | GO:0032268 | 0.0136985 | 1.559841 | 24.8707791 | 36 | 256 | regulation of cellular protein metabolic process |
| 309 | GO:0022414 | 0.0138877 | 1.629808 | 19.9160536 | 30 | 205 | reproductive process |
| 310 | GO:0007600 | 0.0140919 | 2.187322 | 6.7034522 | 13 | 69 | sensory perception |
| 311 | GO:0010803 | 0.0145740 | 9.341797 | 0.5829089 | 3 | 6 | regulation of tumor necrosis factor-mediated signaling pathway |
| 312 | GO:1903265 | 0.0145740 | 9.341797 | 0.5829089 | 3 | 6 | positive regulation of tumor necrosis factor-mediated signaling pathway |
| 313 | GO:0032069 | 0.0145740 | 9.341797 | 0.5829089 | 3 | 6 | regulation of nuclease activity |
| 314 | GO:0032075 | 0.0145740 | 9.341797 | 0.5829089 | 3 | 6 | positive regulation of nuclease activity |
| 315 | GO:0002931 | 0.0145740 | 9.341797 | 0.5829089 | 3 | 6 | response to ischemia |
| 316 | GO:0036010 | 0.0145740 | 9.341797 | 0.5829089 | 3 | 6 | protein localization to endosome |
| 317 | GO:0097305 | 0.0148744 | 2.642416 | 3.9832107 | 9 | 41 | response to alcohol |
| 318 | GO:0001890 | 0.0149765 | 4.255793 | 1.5544237 | 5 | 16 | placenta development |
| 319 | GO:2001236 | 0.0149765 | 4.255793 | 1.5544237 | 5 | 16 | regulation of extrinsic apoptotic signaling pathway |
| 320 | GO:0008038 | 0.0149765 | 4.255793 | 1.5544237 | 5 | 16 | neuron recognition |
| 321 | GO:0002376 | 0.0150403 | 1.664147 | 17.5844180 | 27 | 181 | immune system process |
| 322 | GO:0031327 | 0.0151111 | 1.743138 | 14.3784192 | 23 | 148 | negative regulation of cellular biosynthetic process |
| 323 | GO:0032271 | 0.0151395 | 2.474205 | 4.6632711 | 10 | 48 | regulation of protein polymerization |
| 324 | GO:0051248 | 0.0153019 | 1.889738 | 10.4923599 | 18 | 108 | negative regulation of protein metabolic process |
| 325 | GO:0042981 | 0.0154551 | 1.818959 | 12.0467836 | 20 | 124 | regulation of apoptotic process |
| 326 | GO:0007051 | 0.0157491 | 3.514244 | 2.1373326 | 6 | 22 | spindle organization |
| 327 | GO:0090316 | 0.0157491 | 3.514244 | 2.1373326 | 6 | 22 | positive regulation of intracellular protein transport |
| 328 | GO:1902903 | 0.0165463 | 2.214946 | 6.1205433 | 12 | 63 | regulation of supramolecular fiber organization |
| 329 | GO:1903169 | 0.0166796 | 5.344143 | 1.0686663 | 4 | 11 | regulation of calcium ion transmembrane transport |
| 330 | GO:0045646 | 0.0166796 | 5.344143 | 1.0686663 | 4 | 11 | regulation of erythrocyte differentiation |
| 331 | GO:2001233 | 0.0173560 | 2.561804 | 4.0803622 | 9 | 42 | regulation of apoptotic signaling pathway |
| 332 | GO:0032984 | 0.0174255 | 2.410256 | 4.7604226 | 10 | 49 | protein-containing complex disassembly |
| 333 | GO:0000003 | 0.0183950 | 1.575209 | 21.1790228 | 31 | 218 | reproduction |
| 334 | GO:0071806 | 0.0184048 | 2.983894 | 2.8173929 | 7 | 29 | protein transmembrane transport |
| 335 | GO:0043903 | 0.0184048 | 2.983894 | 2.8173929 | 7 | 29 | regulation of symbiosis, encompassing mutualism through parasitism |
| 336 | GO:0009890 | 0.0188972 | 1.701188 | 14.6698736 | 23 | 151 | negative regulation of biosynthetic process |
| 337 | GO:0009611 | 0.0194123 | 2.248965 | 5.5376344 | 11 | 57 | response to wounding |
| 338 | GO:1903827 | 0.0194123 | 2.248965 | 5.5376344 | 11 | 57 | regulation of cellular protein localization |
| 339 | GO:0051345 | 0.0194123 | 2.248965 | 5.5376344 | 11 | 57 | positive regulation of hydrolase activity |
| 340 | GO:0070507 | 0.0196072 | 3.306830 | 2.2344841 | 6 | 23 | regulation of microtubule cytoskeleton organization |
| 341 | GO:0010822 | 0.0196072 | 3.306830 | 2.2344841 | 6 | 23 | positive regulation of mitochondrion organization |
| 342 | GO:0044087 | 0.0197342 | 1.766827 | 12.3382381 | 20 | 127 | regulation of cellular component biogenesis |
| 343 | GO:0097435 | 0.0198721 | 1.795040 | 11.5610262 | 19 | 119 | supramolecular fiber organization |
| 344 | GO:0050877 | 0.0199115 | 1.827611 | 10.7838144 | 18 | 111 | nervous system process |
| 345 | GO:0001816 | 0.0201266 | 2.485933 | 4.1775137 | 9 | 43 | cytokine production |
| 346 | GO:0001655 | 0.0201266 | 2.485933 | 4.1775137 | 9 | 43 | urogenital system development |
| 347 | GO:0035966 | 0.0201266 | 2.485933 | 4.1775137 | 9 | 43 | response to topologically incorrect protein |
| 348 | GO:0010558 | 0.0207124 | 1.705982 | 13.9898132 | 22 | 144 | negative regulation of macromolecule biosynthetic process |
| 349 | GO:0043067 | 0.0213482 | 1.750093 | 12.4353895 | 20 | 128 | regulation of programmed cell death |
| 350 | GO:0060548 | 0.0214952 | 1.886172 | 9.3265422 | 16 | 96 | negative regulation of cell death |
| 351 | GO:0050778 | 0.0227463 | 2.291717 | 4.9547255 | 10 | 51 | positive regulation of immune response |
| 352 | GO:0045892 | 0.0230621 | 1.733667 | 12.5325410 | 20 | 129 | negative regulation of transcription, DNA-templated |
| 353 | GO:0031101 | 0.0231361 | 4.675147 | 1.1658178 | 4 | 12 | fin regeneration |
| 354 | GO:0042098 | 0.0231361 | 4.675147 | 1.1658178 | 4 | 12 | T cell proliferation |
| 355 | GO:0048585 | 0.0233896 | 1.661159 | 14.9613281 | 23 | 154 | negative regulation of response to stimulus |
| 356 | GO:0043086 | 0.0233943 | 2.090568 | 6.4119977 | 12 | 66 | negative regulation of catalytic activity |
| 357 | GO:0007351 | 0.0236845 | 7.004883 | 0.6800604 | 3 | 7 | tripartite regional subdivision |
| 358 | GO:1902236 | 0.0236845 | 7.004883 | 0.6800604 | 3 | 7 | negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway |
| 359 | GO:0010286 | 0.0236845 | 7.004883 | 0.6800604 | 3 | 7 | heat acclimation |
| 360 | GO:1901019 | 0.0236845 | 7.004883 | 0.6800604 | 3 | 7 | regulation of calcium ion transmembrane transporter activity |
| 361 | GO:0002753 | 0.0236845 | 7.004883 | 0.6800604 | 3 | 7 | cytoplasmic pattern recognition receptor signaling pathway |
| 362 | GO:0008595 | 0.0236845 | 7.004883 | 0.6800604 | 3 | 7 | anterior/posterior axis specification, embryo |
| 363 | GO:0045648 | 0.0236845 | 7.004883 | 0.6800604 | 3 | 7 | positive regulation of erythrocyte differentiation |
| 364 | GO:0045639 | 0.0236845 | 7.004883 | 0.6800604 | 3 | 7 | positive regulation of myeloid cell differentiation |
| 365 | GO:0051246 | 0.0239665 | 1.479167 | 26.7166572 | 37 | 275 | regulation of protein metabolic process |
| 366 | GO:1903828 | 0.0249799 | 3.599547 | 1.7487267 | 5 | 18 | negative regulation of cellular protein localization |
| 367 | GO:0006955 | 0.0256871 | 1.839386 | 9.5208451 | 16 | 98 | immune response |
| 368 | GO:0001894 | 0.0261889 | 2.734088 | 3.0116959 | 7 | 31 | tissue homeostasis |
| 369 | GO:0060433 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | bronchus development |
| 370 | GO:0032958 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | inositol phosphate biosynthetic process |
| 371 | GO:0036270 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | response to diuretic |
| 372 | GO:0042533 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | tumor necrosis factor biosynthetic process |
| 373 | GO:0042534 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | regulation of tumor necrosis factor biosynthetic process |
| 374 | GO:0007354 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | zygotic determination of anterior/posterior axis, embryo |
| 375 | GO:0070424 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | regulation of nucleotide-binding oligomerization domain containing signaling pathway |
| 376 | GO:0070426 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | positive regulation of nucleotide-binding oligomerization domain containing signaling pathway |
| 377 | GO:0070431 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | nucleotide-binding oligomerization domain containing 2 signaling pathway |
| 378 | GO:0070432 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway |
| 379 | GO:0070434 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway |
| 380 | GO:0070194 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | synaptonemal complex disassembly |
| 381 | GO:0007218 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | neuropeptide signaling pathway |
| 382 | GO:0031000 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | response to caffeine |
| 383 | GO:2001240 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | negative regulation of extrinsic apoptotic signaling pathway in absence of ligand |
| 384 | GO:2001239 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | regulation of extrinsic apoptotic signaling pathway in absence of ligand |
| 385 | GO:0097192 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | extrinsic apoptotic signaling pathway in absence of ligand |
| 386 | GO:1902946 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | protein localization to early endosome |
| 387 | GO:1901099 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | negative regulation of signal transduction in absence of ligand |
| 388 | GO:0045109 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | intermediate filament organization |
| 389 | GO:1901894 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | regulation of calcium-transporting ATPase activity |
| 390 | GO:1901896 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | positive regulation of calcium-transporting ATPase activity |
| 391 | GO:0038034 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | signal transduction in absence of ligand |
| 392 | GO:0018992 | 0.0264413 | 18.654971 | 0.2914544 | 2 | 3 | germ-line sex determination |
| 393 | GO:1902679 | 0.0268047 | 1.701702 | 12.7268440 | 20 | 131 | negative regulation of RNA biosynthetic process |
| 394 | GO:1903507 | 0.0268047 | 1.701702 | 12.7268440 | 20 | 131 | negative regulation of nucleic acid-templated transcription |
| 395 | GO:0070585 | 0.0268459 | 2.501512 | 3.6917563 | 8 | 38 | protein localization to mitochondrion |
| 396 | GO:0072655 | 0.0268459 | 2.501512 | 3.6917563 | 8 | 38 | establishment of protein localization to mitochondrion |
| 397 | GO:0007399 | 0.0269273 | 1.442424 | 29.5340502 | 40 | 304 | nervous system development |
| 398 | GO:0044092 | 0.0276224 | 1.910324 | 8.0635729 | 14 | 83 | negative regulation of molecular function |
| 399 | GO:0051179 | 0.0276749 | 1.230281 | 123.6738351 | 142 | 1273 | localization |
| 400 | GO:0051258 | 0.0276906 | 2.109937 | 5.8290889 | 11 | 60 | protein polymerization |
| 401 | GO:0051336 | 0.0278907 | 1.781169 | 10.3952085 | 17 | 107 | regulation of hydrolase activity |
| 402 | GO:2000113 | 0.0282115 | 1.667183 | 13.6012073 | 21 | 140 | negative regulation of cellular macromolecule biosynthetic process |
| 403 | GO:0051253 | 0.0288406 | 1.686147 | 12.8239955 | 20 | 132 | negative regulation of RNA metabolic process |
| 404 | GO:0051050 | 0.0305040 | 1.834675 | 8.9379362 | 15 | 92 | positive regulation of transport |
| 405 | GO:0048869 | 0.0307788 | 1.361204 | 41.2893794 | 53 | 425 | cellular developmental process |
| 406 | GO:0043902 | 0.0308151 | 2.624173 | 3.1088474 | 7 | 32 | positive regulation of multi-organism process |
| 407 | GO:0042119 | 0.0309130 | 4.154816 | 1.2629693 | 4 | 13 | neutrophil activation |
| 408 | GO:0036230 | 0.0309130 | 4.154816 | 1.2629693 | 4 | 13 | granulocyte activation |
| 409 | GO:0007350 | 0.0309130 | 4.154816 | 1.2629693 | 4 | 13 | blastoderm segmentation |
| 410 | GO:0009190 | 0.0309130 | 4.154816 | 1.2629693 | 4 | 13 | cyclic nucleotide biosynthetic process |
| 411 | GO:0002444 | 0.0309130 | 4.154816 | 1.2629693 | 4 | 13 | myeloid leukocyte mediated immunity |
| 412 | GO:0002446 | 0.0309130 | 4.154816 | 1.2629693 | 4 | 13 | neutrophil mediated immunity |
| 413 | GO:0009187 | 0.0309130 | 4.154816 | 1.2629693 | 4 | 13 | cyclic nucleotide metabolic process |
| 414 | GO:0042594 | 0.0310104 | 2.420309 | 3.7889078 | 8 | 39 | response to starvation |
| 415 | GO:0009416 | 0.0310104 | 2.420309 | 3.7889078 | 8 | 39 | response to light stimulus |
| 416 | GO:0032273 | 0.0310104 | 2.420309 | 3.7889078 | 8 | 39 | positive regulation of protein polymerization |
| 417 | GO:0051924 | 0.0312733 | 3.341737 | 1.8458781 | 5 | 19 | regulation of calcium ion transport |
| 418 | GO:2001243 | 0.0312733 | 3.341737 | 1.8458781 | 5 | 19 | negative regulation of intrinsic apoptotic signaling pathway |
| 419 | GO:0097191 | 0.0312733 | 3.341737 | 1.8458781 | 5 | 19 | extrinsic apoptotic signaling pathway |
| 420 | GO:0030218 | 0.0312733 | 3.341737 | 1.8458781 | 5 | 19 | erythrocyte differentiation |
| 421 | GO:0002262 | 0.0312733 | 3.341737 | 1.8458781 | 5 | 19 | myeloid cell homeostasis |
| 422 | GO:0035303 | 0.0312733 | 3.341737 | 1.8458781 | 5 | 19 | regulation of dephosphorylation |
| 423 | GO:0034101 | 0.0312733 | 3.341737 | 1.8458781 | 5 | 19 | erythrocyte homeostasis |
| 424 | GO:0048523 | 0.0321128 | 1.342633 | 44.9811356 | 57 | 463 | negative regulation of cellular process |
| 425 | GO:0061061 | 0.0330845 | 1.773335 | 9.8122996 | 16 | 101 | muscle structure development |
| 426 | GO:0030154 | 0.0337976 | 1.359492 | 39.7349557 | 51 | 409 | cell differentiation |
| 427 | GO:0042060 | 0.0344215 | 2.222384 | 4.5661196 | 9 | 47 | wound healing |
| 428 | GO:0009581 | 0.0348872 | 2.809037 | 2.5259385 | 6 | 26 | detection of external stimulus |
| 429 | GO:0009582 | 0.0348872 | 2.809037 | 2.5259385 | 6 | 26 | detection of abiotic stimulus |
| 430 | GO:0060711 | 0.0352056 | 5.602734 | 0.7772118 | 3 | 8 | labyrinthine layer development |
| 431 | GO:1902235 | 0.0352056 | 5.602734 | 0.7772118 | 3 | 8 | regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway |
| 432 | GO:0033209 | 0.0352056 | 5.602734 | 0.7772118 | 3 | 8 | tumor necrosis factor-mediated signaling pathway |
| 433 | GO:0007602 | 0.0352056 | 5.602734 | 0.7772118 | 3 | 8 | phototransduction |
| 434 | GO:0006298 | 0.0352056 | 5.602734 | 0.7772118 | 3 | 8 | mismatch repair |
| 435 | GO:0001817 | 0.0355969 | 2.344181 | 3.8860592 | 8 | 40 | regulation of cytokine production |
| 436 | GO:0030001 | 0.0356499 | 1.641107 | 13.1154499 | 20 | 135 | metal ion transport |
| 437 | GO:0007033 | 0.0359599 | 2.522714 | 3.2059989 | 7 | 33 | vacuole organization |
| 438 | GO:0060341 | 0.0361791 | 1.787468 | 9.1322392 | 15 | 94 | regulation of cellular localization |
| 439 | GO:1901701 | 0.0362689 | 1.829563 | 8.3550274 | 14 | 86 | cellular response to oxygen-containing compound |
| 440 | GO:0006810 | 0.0365383 | 1.226460 | 106.6723260 | 123 | 1098 | transport |
| 441 | GO:0051234 | 0.0380542 | 1.221677 | 109.6840219 | 126 | 1129 | establishment of localization |
| 442 | GO:0051247 | 0.0381651 | 1.626611 | 13.2126014 | 20 | 136 | positive regulation of protein metabolic process |
| 443 | GO:0002684 | 0.0382497 | 1.986951 | 6.1205433 | 11 | 63 | positive regulation of immune system process |
| 444 | GO:0010605 | 0.0388499 | 1.423591 | 26.8138087 | 36 | 276 | negative regulation of macromolecule metabolic process |
| 445 | GO:0032943 | 0.0400461 | 3.738552 | 1.3601207 | 4 | 14 | mononuclear cell proliferation |
| 446 | GO:0070661 | 0.0400461 | 3.738552 | 1.3601207 | 4 | 14 | leukocyte proliferation |
| 447 | GO:0046651 | 0.0400461 | 3.738552 | 1.3601207 | 4 | 14 | lymphocyte proliferation |
| 448 | GO:1903321 | 0.0400461 | 3.738552 | 1.3601207 | 4 | 14 | negative regulation of protein modification by small protein conjugation or removal |
| 449 | GO:0035304 | 0.0400461 | 3.738552 | 1.3601207 | 4 | 14 | regulation of protein dephosphorylation |
| 450 | GO:0014706 | 0.0410174 | 2.040465 | 5.4404829 | 10 | 56 | striated muscle tissue development |
| 451 | GO:0022008 | 0.0412701 | 1.475729 | 20.8875684 | 29 | 215 | neurogenesis |
| 452 | GO:0010821 | 0.0413101 | 2.674712 | 2.6230900 | 6 | 27 | regulation of mitochondrion organization |
| 453 | GO:0032388 | 0.0413101 | 2.674712 | 2.6230900 | 6 | 27 | positive regulation of intracellular transport |
| 454 | GO:0031399 | 0.0428127 | 1.531788 | 16.7100547 | 24 | 172 | regulation of protein modification process |
| 455 | GO:0033365 | 0.0431715 | 1.646657 | 11.7553292 | 18 | 121 | protein localization to organelle |
| 456 | GO:0048519 | 0.0443329 | 1.289811 | 53.1418600 | 65 | 547 | negative regulation of biological process |
| 457 | GO:0032270 | 0.0449481 | 1.613357 | 12.6296925 | 19 | 130 | positive regulation of cellular protein metabolic process |
| 458 | GO:0043254 | 0.0456143 | 1.996630 | 5.5376344 | 10 | 57 | regulation of protein complex assembly |
| 459 | GO:0048584 | 0.0461335 | 1.504290 | 17.6815695 | 25 | 182 | positive regulation of response to stimulus |
| 460 | GO:0065009 | 0.0466520 | 1.413101 | 25.4536880 | 34 | 262 | regulation of molecular function |
| 461 | GO:0051169 | 0.0466814 | 1.912551 | 6.3148463 | 11 | 65 | nuclear transport |
| 462 | GO:0048871 | 0.0478755 | 2.341535 | 3.4003018 | 7 | 35 | multicellular organismal homeostasis |
| 463 | GO:1903829 | 0.0478755 | 2.341535 | 3.4003018 | 7 | 35 | positive regulation of cellular protein localization |
| 464 | GO:0009792 | 0.0487092 | 1.673035 | 10.2980570 | 16 | 106 | embryo development ending in birth or egg hatching |
| 465 | GO:0010038 | 0.0489077 | 2.058469 | 4.8575740 | 9 | 50 | response to metal ion |
| 466 | GO:0071356 | 0.0490812 | 4.667969 | 0.8743633 | 3 | 9 | cellular response to tumor necrosis factor |
| 467 | GO:0070059 | 0.0490812 | 4.667969 | 0.8743633 | 3 | 9 | intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress |
| 468 | GO:0031397 | 0.0490812 | 4.667969 | 0.8743633 | 3 | 9 | negative regulation of protein ubiquitination |
| 469 | GO:1903708 | 0.0490812 | 4.667969 | 0.8743633 | 3 | 9 | positive regulation of hemopoiesis |
| 470 | GO:1904376 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | negative regulation of protein localization to cell periphery |
| 471 | GO:1902044 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | regulation of Fas signaling pathway |
| 472 | GO:1902045 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | negative regulation of Fas signaling pathway |
| 473 | GO:0036337 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | Fas signaling pathway |
| 474 | GO:0060710 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | chorio-allantoic fusion |
| 475 | GO:0060715 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | syncytiotrophoblast cell differentiation involved in labyrinthine layer development |
| 476 | GO:0050962 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | detection of light stimulus involved in sensory perception |
| 477 | GO:0050921 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | positive regulation of chemotaxis |
| 478 | GO:0050908 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | detection of light stimulus involved in visual perception |
| 479 | GO:0070423 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | nucleotide-binding oligomerization domain containing signaling pathway |
| 480 | GO:0007422 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | peripheral nervous system development |
| 481 | GO:0007530 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | sex determination |
| 482 | GO:0007603 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | phototransduction, visible light |
| 483 | GO:0043101 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | purine-containing compound salvage |
| 484 | GO:1903077 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | negative regulation of protein localization to plasma membrane |
| 485 | GO:0015697 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | quaternary ammonium group transport |
| 486 | GO:2000514 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | regulation of CD4-positive, alpha-beta T cell activation |
| 487 | GO:2000504 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | positive regulation of blood vessel remodeling |
| 488 | GO:0072132 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | mesenchyme morphogenesis |
| 489 | GO:0006013 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | mannose metabolic process |
| 490 | GO:0016056 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | rhodopsin mediated signaling pathway |
| 491 | GO:0035710 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | CD4-positive, alpha-beta T cell activation |
| 492 | GO:0035872 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway |
| 493 | GO:0032469 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | endoplasmic reticulum calcium ion homeostasis |
| 494 | GO:1905476 | 0.0494985 | 9.325536 | 0.3886059 | 2 | 4 | negative regulation of protein localization to membrane |
Module 5
GO_term_green <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_green.csv")
GO_term_green %>%
kbl() %>%
kable_styling(bootstrap_options = "striped", full_width = F, position = "left") %>%
kable_paper() %>%
scroll_box(width = "800px", height = "200px")| X | GOBPID | Pvalue | OddsRatio | ExpCount | Count | Size | Term |
|---|---|---|---|---|---|---|---|
| 1 | GO:0055114 | 0.0000000 | 3.874922 | 14.1482739 | 43 | 300 | oxidation-reduction process |
| 2 | GO:0006629 | 0.0000000 | 3.294290 | 13.6766648 | 37 | 290 | lipid metabolic process |
| 3 | GO:0044255 | 0.0000026 | 3.177618 | 9.6208263 | 26 | 204 | cellular lipid metabolic process |
| 4 | GO:0006720 | 0.0000044 | 9.393983 | 1.3676665 | 9 | 29 | isoprenoid metabolic process |
| 5 | GO:0044281 | 0.0000046 | 2.357653 | 21.3167327 | 43 | 452 | small molecule metabolic process |
| 6 | GO:0019752 | 0.0000070 | 3.059636 | 9.5265044 | 25 | 202 | carboxylic acid metabolic process |
| 7 | GO:0043436 | 0.0000084 | 3.024209 | 9.6208263 | 25 | 204 | oxoacid metabolic process |
| 8 | GO:0006082 | 0.0000084 | 3.024209 | 9.6208263 | 25 | 204 | organic acid metabolic process |
| 9 | GO:0006066 | 0.0000108 | 8.163810 | 1.5091492 | 9 | 32 | alcohol metabolic process |
| 10 | GO:0055085 | 0.0000122 | 2.273595 | 21.4110545 | 42 | 454 | transmembrane transport |
| 11 | GO:0034754 | 0.0000465 | 20.595918 | 0.4716091 | 5 | 10 | cellular hormone metabolic process |
| 12 | GO:0032787 | 0.0000742 | 4.417514 | 3.2541030 | 12 | 69 | monocarboxylic acid metabolic process |
| 13 | GO:1901615 | 0.0000902 | 4.698318 | 2.8296548 | 11 | 60 | organic hydroxy compound metabolic process |
| 14 | GO:0106120 | 0.0001037 | Inf | 0.1414827 | 3 | 3 | positive regulation of sterol biosynthetic process |
| 15 | GO:0045940 | 0.0001037 | Inf | 0.1414827 | 3 | 3 | positive regulation of steroid metabolic process |
| 16 | GO:0010893 | 0.0001037 | Inf | 0.1414827 | 3 | 3 | positive regulation of steroid biosynthetic process |
| 17 | GO:1902932 | 0.0001037 | Inf | 0.1414827 | 3 | 3 | positive regulation of alcohol biosynthetic process |
| 18 | GO:0090205 | 0.0001037 | Inf | 0.1414827 | 3 | 3 | positive regulation of cholesterol metabolic process |
| 19 | GO:0045542 | 0.0001037 | Inf | 0.1414827 | 3 | 3 | positive regulation of cholesterol biosynthetic process |
| 20 | GO:0006631 | 0.0001375 | 5.510496 | 2.0279193 | 9 | 43 | fatty acid metabolic process |
| 21 | GO:0008610 | 0.0001393 | 3.252466 | 5.6593096 | 16 | 120 | lipid biosynthetic process |
| 22 | GO:0016042 | 0.0003325 | 4.799234 | 2.2637238 | 9 | 48 | lipid catabolic process |
| 23 | GO:0090181 | 0.0004003 | 61.336032 | 0.1886437 | 3 | 4 | regulation of cholesterol metabolic process |
| 24 | GO:0045540 | 0.0004003 | 61.336032 | 0.1886437 | 3 | 4 | regulation of cholesterol biosynthetic process |
| 25 | GO:0042445 | 0.0004081 | 7.738217 | 1.0375401 | 6 | 22 | hormone metabolic process |
| 26 | GO:0006732 | 0.0005438 | 3.703536 | 3.4427467 | 11 | 73 | coenzyme metabolic process |
| 27 | GO:0001523 | 0.0008096 | 13.672087 | 0.4716091 | 4 | 10 | retinoid metabolic process |
| 28 | GO:0009074 | 0.0008096 | 13.672087 | 0.4716091 | 4 | 10 | aromatic amino acid family catabolic process |
| 29 | GO:0016126 | 0.0008096 | 13.672087 | 0.4716091 | 4 | 10 | sterol biosynthetic process |
| 30 | GO:0016101 | 0.0008096 | 13.672087 | 0.4716091 | 4 | 10 | diterpenoid metabolic process |
| 31 | GO:0045834 | 0.0008096 | 13.672087 | 0.4716091 | 4 | 10 | positive regulation of lipid metabolic process |
| 32 | GO:0009108 | 0.0008231 | 4.154357 | 2.5466893 | 9 | 54 | coenzyme biosynthetic process |
| 33 | GO:0008202 | 0.0008581 | 5.360158 | 1.6034710 | 7 | 34 | steroid metabolic process |
| 34 | GO:0006694 | 0.0008598 | 6.512511 | 1.1790228 | 6 | 25 | steroid biosynthetic process |
| 35 | GO:0106118 | 0.0009658 | 30.661943 | 0.2358046 | 3 | 5 | regulation of sterol biosynthetic process |
| 36 | GO:0050810 | 0.0009658 | 30.661943 | 0.2358046 | 3 | 5 | regulation of steroid biosynthetic process |
| 37 | GO:0046889 | 0.0009658 | 30.661943 | 0.2358046 | 3 | 5 | positive regulation of lipid biosynthetic process |
| 38 | GO:1902930 | 0.0009658 | 30.661943 | 0.2358046 | 3 | 5 | regulation of alcohol biosynthetic process |
| 39 | GO:0019218 | 0.0009658 | 30.661943 | 0.2358046 | 3 | 5 | regulation of steroid metabolic process |
| 40 | GO:0006695 | 0.0009658 | 30.661943 | 0.2358046 | 3 | 5 | cholesterol biosynthetic process |
| 41 | GO:0046395 | 0.0010302 | 5.167695 | 1.6506320 | 7 | 35 | carboxylic acid catabolic process |
| 42 | GO:0016054 | 0.0010302 | 5.167695 | 1.6506320 | 7 | 35 | organic acid catabolic process |
| 43 | GO:1901605 | 0.0010321 | 4.479786 | 2.1222411 | 8 | 45 | alpha-amino acid metabolic process |
| 44 | GO:0006721 | 0.0012254 | 11.716609 | 0.5187700 | 4 | 11 | terpenoid metabolic process |
| 45 | GO:0044242 | 0.0012283 | 4.988506 | 1.6977929 | 7 | 36 | cellular lipid catabolic process |
| 46 | GO:0044282 | 0.0013877 | 4.248358 | 2.2165629 | 8 | 47 | small molecule catabolic process |
| 47 | GO:1901617 | 0.0019679 | 5.375624 | 1.3676665 | 6 | 29 | organic hydroxy compound biosynthetic process |
| 48 | GO:0051186 | 0.0021753 | 2.743724 | 5.2820223 | 13 | 112 | cofactor metabolic process |
| 49 | GO:0097089 | 0.0022157 | Inf | 0.0943218 | 2 | 2 | methyl-branched fatty acid metabolic process |
| 50 | GO:0001561 | 0.0022157 | Inf | 0.0943218 | 2 | 2 | fatty acid alpha-oxidation |
| 51 | GO:0006103 | 0.0022157 | Inf | 0.0943218 | 2 | 2 | 2-oxoglutarate metabolic process |
| 52 | GO:0062013 | 0.0031493 | 15.324899 | 0.3301264 | 3 | 7 | positive regulation of small molecule metabolic process |
| 53 | GO:1902653 | 0.0031493 | 15.324899 | 0.3301264 | 3 | 7 | secondary alcohol biosynthetic process |
| 54 | GO:0008203 | 0.0031493 | 15.324899 | 0.3301264 | 3 | 7 | cholesterol metabolic process |
| 55 | GO:0016125 | 0.0033226 | 8.196748 | 0.6602528 | 4 | 14 | sterol metabolic process |
| 56 | GO:0006576 | 0.0033226 | 8.196748 | 0.6602528 | 4 | 14 | cellular biogenic amine metabolic process |
| 57 | GO:0051188 | 0.0042917 | 3.159716 | 3.2069421 | 9 | 68 | cofactor biosynthetic process |
| 58 | GO:0046165 | 0.0056075 | 6.827913 | 0.7545746 | 4 | 16 | alcohol biosynthetic process |
| 59 | GO:0008299 | 0.0056075 | 6.827913 | 0.7545746 | 4 | 16 | isoprenoid biosynthetic process |
| 60 | GO:0036367 | 0.0064396 | 40.725806 | 0.1414827 | 2 | 3 | light adaption |
| 61 | GO:0023058 | 0.0064396 | 40.725806 | 0.1414827 | 2 | 3 | adaptation of signaling pathway |
| 62 | GO:0052803 | 0.0064396 | 40.725806 | 0.1414827 | 2 | 3 | imidazole-containing compound metabolic process |
| 63 | GO:0052805 | 0.0064396 | 40.725806 | 0.1414827 | 2 | 3 | imidazole-containing compound catabolic process |
| 64 | GO:0016062 | 0.0064396 | 40.725806 | 0.1414827 | 2 | 3 | adaptation of rhodopsin mediated signaling |
| 65 | GO:0009644 | 0.0064396 | 40.725806 | 0.1414827 | 2 | 3 | response to high light intensity |
| 66 | GO:0006563 | 0.0064396 | 40.725806 | 0.1414827 | 2 | 3 | L-serine metabolic process |
| 67 | GO:0006547 | 0.0064396 | 40.725806 | 0.1414827 | 2 | 3 | histidine metabolic process |
| 68 | GO:0006548 | 0.0064396 | 40.725806 | 0.1414827 | 2 | 3 | histidine catabolic process |
| 69 | GO:1902652 | 0.0070443 | 10.212551 | 0.4244482 | 3 | 9 | secondary alcohol metabolic process |
| 70 | GO:0034308 | 0.0070443 | 10.212551 | 0.4244482 | 3 | 9 | primary alcohol metabolic process |
| 71 | GO:0044283 | 0.0070626 | 2.446367 | 5.3763441 | 12 | 114 | small molecule biosynthetic process |
| 72 | GO:0009072 | 0.0070654 | 6.301438 | 0.8017355 | 4 | 17 | aromatic amino acid family metabolic process |
| 73 | GO:0006081 | 0.0087533 | 5.850174 | 0.8488964 | 4 | 18 | cellular aldehyde metabolic process |
| 74 | GO:0006665 | 0.0087533 | 5.850174 | 0.8488964 | 4 | 18 | sphingolipid metabolic process |
| 75 | GO:0006520 | 0.0100716 | 2.427090 | 4.9518959 | 11 | 105 | cellular amino acid metabolic process |
| 76 | GO:0097164 | 0.0105011 | 4.274660 | 1.3676665 | 5 | 29 | ammonium ion metabolic process |
| 77 | GO:0009308 | 0.0106845 | 5.459079 | 0.8960573 | 4 | 19 | amine metabolic process |
| 78 | GO:1901607 | 0.0106845 | 5.459079 | 0.8960573 | 4 | 19 | alpha-amino acid biosynthetic process |
| 79 | GO:0044106 | 0.0106845 | 5.459079 | 0.8960573 | 4 | 19 | cellular amine metabolic process |
| 80 | GO:0042572 | 0.0124790 | 20.358871 | 0.1886437 | 2 | 4 | retinol metabolic process |
| 81 | GO:0042574 | 0.0124790 | 20.358871 | 0.1886437 | 2 | 4 | retinal metabolic process |
| 82 | GO:0046473 | 0.0124790 | 20.358871 | 0.1886437 | 2 | 4 | phosphatidic acid metabolic process |
| 83 | GO:0007603 | 0.0124790 | 20.358871 | 0.1886437 | 2 | 4 | phototransduction, visible light |
| 84 | GO:0043545 | 0.0124790 | 20.358871 | 0.1886437 | 2 | 4 | molybdopterin cofactor metabolic process |
| 85 | GO:0019720 | 0.0124790 | 20.358871 | 0.1886437 | 2 | 4 | Mo-molybdopterin cofactor metabolic process |
| 86 | GO:0016056 | 0.0124790 | 20.358871 | 0.1886437 | 2 | 4 | rhodopsin mediated signaling pathway |
| 87 | GO:0032367 | 0.0124790 | 20.358871 | 0.1886437 | 2 | 4 | intracellular cholesterol transport |
| 88 | GO:0051189 | 0.0124790 | 20.358871 | 0.1886437 | 2 | 4 | prosthetic group metabolic process |
| 89 | GO:0006777 | 0.0124790 | 20.358871 | 0.1886437 | 2 | 4 | Mo-molybdopterin cofactor biosynthetic process |
| 90 | GO:0006654 | 0.0124790 | 20.358871 | 0.1886437 | 2 | 4 | phosphatidic acid biosynthetic process |
| 91 | GO:0006685 | 0.0124790 | 20.358871 | 0.1886437 | 2 | 4 | sphingomyelin catabolic process |
| 92 | GO:0008652 | 0.0128711 | 5.116870 | 0.9432183 | 4 | 20 | cellular amino acid biosynthetic process |
| 93 | GO:1901606 | 0.0128711 | 5.116870 | 0.9432183 | 4 | 20 | alpha-amino acid catabolic process |
| 94 | GO:0019395 | 0.0129005 | 7.656377 | 0.5187700 | 3 | 11 | fatty acid oxidation |
| 95 | GO:0034440 | 0.0129005 | 7.656377 | 0.5187700 | 3 | 11 | lipid oxidation |
| 96 | GO:0009062 | 0.0166104 | 6.804318 | 0.5659310 | 3 | 12 | fatty acid catabolic process |
| 97 | GO:0007186 | 0.0189731 | 2.107819 | 6.1309187 | 12 | 130 | G protein-coupled receptor signaling pathway |
| 98 | GO:0046394 | 0.0200228 | 2.769310 | 2.7824939 | 7 | 59 | carboxylic acid biosynthetic process |
| 99 | GO:0016053 | 0.0200228 | 2.769310 | 2.7824939 | 7 | 59 | organic acid biosynthetic process |
| 100 | GO:2001238 | 0.0201544 | 13.569892 | 0.2358046 | 2 | 5 | positive regulation of extrinsic apoptotic signaling pathway |
| 101 | GO:0006684 | 0.0201544 | 13.569892 | 0.2358046 | 2 | 5 | sphingomyelin metabolic process |
| 102 | GO:0072329 | 0.0208545 | 6.122672 | 0.6130919 | 3 | 13 | monocarboxylic acid catabolic process |
| 103 | GO:0043648 | 0.0208545 | 6.122672 | 0.6130919 | 3 | 13 | dicarboxylic acid metabolic process |
| 104 | GO:0009063 | 0.0210631 | 4.306376 | 1.0847010 | 4 | 23 | cellular amino acid catabolic process |
| 105 | GO:1901071 | 0.0241283 | 2.932670 | 2.2637238 | 6 | 48 | glucosamine-containing compound metabolic process |
| 106 | GO:0046890 | 0.0256359 | 5.564961 | 0.6602528 | 3 | 14 | regulation of lipid biosynthetic process |
| 107 | GO:0010817 | 0.0264481 | 2.863896 | 2.3108847 | 6 | 49 | regulation of hormone levels |
| 108 | GO:0006040 | 0.0264481 | 2.863896 | 2.3108847 | 6 | 49 | amino sugar metabolic process |
| 109 | GO:0042401 | 0.0292995 | 10.175403 | 0.2829655 | 2 | 6 | cellular biogenic amine biosynthetic process |
| 110 | GO:0042559 | 0.0292995 | 10.175403 | 0.2829655 | 2 | 6 | pteridine-containing compound biosynthetic process |
| 111 | GO:0009070 | 0.0292995 | 10.175403 | 0.2829655 | 2 | 6 | serine family amino acid biosynthetic process |
| 112 | GO:0009309 | 0.0292995 | 10.175403 | 0.2829655 | 2 | 6 | amine biosynthetic process |
| 113 | GO:0009435 | 0.0292995 | 10.175403 | 0.2829655 | 2 | 6 | NAD biosynthetic process |
| 114 | GO:0009642 | 0.0292995 | 10.175403 | 0.2829655 | 2 | 6 | response to light intensity |
| 115 | GO:0032366 | 0.0292995 | 10.175403 | 0.2829655 | 2 | 6 | intracellular sterol transport |
| 116 | GO:0006595 | 0.0292995 | 10.175403 | 0.2829655 | 2 | 6 | polyamine metabolic process |
| 117 | GO:0006596 | 0.0292995 | 10.175403 | 0.2829655 | 2 | 6 | polyamine biosynthetic process |
| 118 | GO:0009064 | 0.0309536 | 5.100202 | 0.7074137 | 3 | 15 | glutamine family amino acid metabolic process |
| 119 | GO:0006643 | 0.0315157 | 3.103278 | 1.7921147 | 5 | 38 | membrane lipid metabolic process |
| 120 | GO:0019216 | 0.0360606 | 3.554613 | 1.2733447 | 4 | 27 | regulation of lipid metabolic process |
| 121 | GO:0009084 | 0.0397595 | 8.138710 | 0.3301264 | 2 | 7 | glutamine family amino acid biosynthetic process |
| 122 | GO:0045494 | 0.0397595 | 8.138710 | 0.3301264 | 2 | 7 | photoreceptor cell maintenance |
| 123 | GO:0006767 | 0.0397595 | 8.138710 | 0.3301264 | 2 | 7 | water-soluble vitamin metabolic process |
| 124 | GO:0048047 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | mating behavior, sex discrimination |
| 125 | GO:0045924 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | regulation of female receptivity |
| 126 | GO:0045916 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | negative regulation of complement activation |
| 127 | GO:0045938 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | positive regulation of circadian sleep/wake cycle, sleep |
| 128 | GO:1904109 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | positive regulation of cholesterol import |
| 129 | GO:0060180 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | female mating behavior |
| 130 | GO:0042822 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | pyridoxal phosphate metabolic process |
| 131 | GO:0042823 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | pyridoxal phosphate biosynthetic process |
| 132 | GO:0042573 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | retinoic acid metabolic process |
| 133 | GO:0046497 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | nicotinate nucleotide metabolic process |
| 134 | GO:0060620 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | regulation of cholesterol import |
| 135 | GO:0000103 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | sulfate assimilation |
| 136 | GO:0033344 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | cholesterol efflux |
| 137 | GO:0070508 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | cholesterol import |
| 138 | GO:0007621 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | negative regulation of female receptivity |
| 139 | GO:0043446 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | cellular alkane metabolic process |
| 140 | GO:0043447 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | alkane biosynthetic process |
| 141 | GO:2000258 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | negative regulation of protein activation cascade |
| 142 | GO:0010955 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | negative regulation of protein processing |
| 143 | GO:0002378 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | immunoglobulin biosynthetic process |
| 144 | GO:0019365 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | pyridine nucleotide salvage |
| 145 | GO:0019357 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | nicotinate nucleotide biosynthetic process |
| 146 | GO:0019358 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | nicotinate nucleotide salvage |
| 147 | GO:0019310 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | inositol catabolic process |
| 148 | GO:0019343 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | cysteine biosynthetic process via cystathionine |
| 149 | GO:0019344 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | cysteine biosynthetic process |
| 150 | GO:0009443 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | pyridoxal 5’-phosphate salvage |
| 151 | GO:1903318 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | negative regulation of protein maturation |
| 152 | GO:0002138 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | retinoic acid biosynthetic process |
| 153 | GO:0035376 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | sterol import |
| 154 | GO:0043606 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | formamide metabolic process |
| 155 | GO:2000911 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | positive regulation of sterol import |
| 156 | GO:2000909 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | regulation of sterol import |
| 157 | GO:0019852 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | L-ascorbic acid metabolic process |
| 158 | GO:0019556 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | histidine catabolic process to glutamate and formamide |
| 159 | GO:0008295 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | spermidine biosynthetic process |
| 160 | GO:0008216 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | spermidine metabolic process |
| 161 | GO:0032380 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | regulation of intracellular sterol transport |
| 162 | GO:0032382 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | positive regulation of intracellular sterol transport |
| 163 | GO:0032383 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | regulation of intracellular cholesterol transport |
| 164 | GO:0032385 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | positive regulation of intracellular cholesterol transport |
| 165 | GO:0032373 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | positive regulation of sterol transport |
| 166 | GO:0032376 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | positive regulation of cholesterol transport |
| 167 | GO:0032377 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | regulation of intracellular lipid transport |
| 168 | GO:0032379 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | positive regulation of intracellular lipid transport |
| 169 | GO:0016102 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | diterpenoid biosynthetic process |
| 170 | GO:0034699 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | response to luteinizing hormone |
| 171 | GO:0006535 | 0.0471609 | Inf | 0.0471609 | 1 | 1 | cysteine biosynthetic process from serine |
Module 6
GO_term_red <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_red.csv")
GO_term_red %>%
kbl() %>%
kable_styling(bootstrap_options = "striped", full_width = F, position = "left") %>%
kable_paper() %>%
scroll_box(width = "800px", height = "200px")| X | GOBPID | Pvalue | OddsRatio | ExpCount | Count | Size | Term |
|---|---|---|---|---|---|---|---|
| 1 | GO:0006412 | 0.0000318 | 4.194114 | 3.9675533 | 14 | 239 | translation |
| 2 | GO:0043043 | 0.0000366 | 4.136439 | 4.0173552 | 14 | 242 | peptide biosynthetic process |
| 3 | GO:0043604 | 0.0000652 | 3.903106 | 4.2331636 | 14 | 255 | amide biosynthetic process |
| 4 | GO:0043603 | 0.0001179 | 3.500972 | 5.0465950 | 15 | 304 | cellular amide metabolic process |
| 5 | GO:0006518 | 0.0001258 | 3.648333 | 4.4987738 | 14 | 271 | peptide metabolic process |
| 6 | GO:0045833 | 0.0002725 | Inf | 0.0332013 | 2 | 2 | negative regulation of lipid metabolic process |
| 7 | GO:0016032 | 0.0034029 | 7.253501 | 0.6308244 | 4 | 38 | viral process |
| 8 | GO:0019079 | 0.0041085 | 10.787543 | 0.3320128 | 3 | 20 | viral genome replication |
| 9 | GO:1901566 | 0.0041428 | 2.266955 | 8.5493303 | 17 | 515 | organonitrogen compound biosynthetic process |
| 10 | GO:0009267 | 0.0047363 | 10.186274 | 0.3486135 | 3 | 21 | cellular response to starvation |
| 11 | GO:0031669 | 0.0054189 | 9.648297 | 0.3652141 | 3 | 22 | cellular response to nutrient levels |
| 12 | GO:0031668 | 0.0061578 | 9.164118 | 0.3818148 | 3 | 23 | cellular response to extracellular stimulus |
| 13 | GO:0044403 | 0.0062901 | 6.006969 | 0.7470289 | 4 | 45 | symbiont process |
| 14 | GO:0044419 | 0.0073434 | 5.725360 | 0.7802301 | 4 | 47 | interspecies interaction between organisms |
| 15 | GO:0010467 | 0.0081218 | 1.781539 | 21.5476325 | 32 | 1298 | gene expression |
| 16 | GO:0071496 | 0.0107316 | 7.324235 | 0.4648180 | 3 | 28 | cellular response to external stimulus |
| 17 | GO:0019058 | 0.0107316 | 7.324235 | 0.4648180 | 3 | 28 | viral life cycle |
| 18 | GO:0046916 | 0.0135963 | 13.447028 | 0.1826071 | 2 | 11 | cellular transition metal ion homeostasis |
| 19 | GO:0048507 | 0.0161410 | 12.100000 | 0.1992077 | 2 | 12 | meristem development |
| 20 | GO:0000724 | 0.0161410 | 12.100000 | 0.1992077 | 2 | 12 | double-strand break repair via homologous recombination |
| 21 | GO:0000725 | 0.0161410 | 12.100000 | 0.1992077 | 2 | 12 | recombinational repair |
| 22 | GO:0038158 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | granulocyte colony-stimulating factor signaling pathway |
| 23 | GO:0044828 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation by host of viral genome replication |
| 24 | GO:1904398 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | positive regulation of neuromuscular junction development |
| 25 | GO:0045953 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of natural killer cell mediated cytotoxicity |
| 26 | GO:0032692 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of interleukin-1 production |
| 27 | GO:0006924 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | activation-induced cell death of T cells |
| 28 | GO:0044528 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | regulation of mitochondrial mRNA stability |
| 29 | GO:0050819 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of coagulation |
| 30 | GO:0055108 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | Golgi to transport vesicle transport |
| 31 | GO:0048341 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | paraxial mesoderm formation |
| 32 | GO:0048305 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | immunoglobulin secretion |
| 33 | GO:0050995 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of lipid catabolic process |
| 34 | GO:0070341 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | fat cell proliferation |
| 35 | GO:0070342 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | brown fat cell proliferation |
| 36 | GO:0070344 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | regulation of fat cell proliferation |
| 37 | GO:0070345 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of fat cell proliferation |
| 38 | GO:0070347 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | regulation of brown fat cell proliferation |
| 39 | GO:0070348 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of brown fat cell proliferation |
| 40 | GO:0007110 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | meiosis I cytokinesis |
| 41 | GO:0048521 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of behavior |
| 42 | GO:0048541 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | Peyer’s patch development |
| 43 | GO:0048537 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | mucosal-associated lymphoid tissue development |
| 44 | GO:0070230 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | positive regulation of lymphocyte apoptotic process |
| 45 | GO:0070234 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | positive regulation of T cell apoptotic process |
| 46 | GO:0070235 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | regulation of activation-induced cell death of T cells |
| 47 | GO:0070237 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | positive regulation of activation-induced cell death of T cells |
| 48 | GO:0010152 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | pollen maturation |
| 49 | GO:0046851 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of bone remodeling |
| 50 | GO:0070836 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | caveola assembly |
| 51 | GO:2001212 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | regulation of vasculogenesis |
| 52 | GO:2001214 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | positive regulation of vasculogenesis |
| 53 | GO:0090330 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | regulation of platelet aggregation |
| 54 | GO:0090331 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of platelet aggregation |
| 55 | GO:0001911 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of leukocyte mediated cytotoxicity |
| 56 | GO:0046641 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | positive regulation of alpha-beta T cell proliferation |
| 57 | GO:0031342 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of cell killing |
| 58 | GO:0010543 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | regulation of platelet activation |
| 59 | GO:0010544 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of platelet activation |
| 60 | GO:0015761 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | mannose transmembrane transport |
| 61 | GO:2000108 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | positive regulation of leukocyte apoptotic process |
| 62 | GO:2000252 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of feeding behavior |
| 63 | GO:0019085 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | early viral transcription |
| 64 | GO:0019086 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | late viral transcription |
| 65 | GO:0000957 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | mitochondrial RNA catabolic process |
| 66 | GO:0000958 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | mitochondrial mRNA catabolic process |
| 67 | GO:0002347 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | response to tumor cell |
| 68 | GO:2000563 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | positive regulation of CD4-positive, alpha-beta T cell proliferation |
| 69 | GO:0030195 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of blood coagulation |
| 70 | GO:0002420 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | natural killer cell mediated cytotoxicity directed against tumor cell target |
| 71 | GO:0002423 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | natural killer cell mediated immune response to tumor cell |
| 72 | GO:0002418 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | immune response to tumor cell |
| 73 | GO:0035457 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | cellular response to interferon-alpha |
| 74 | GO:0002716 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of natural killer cell mediated immunity |
| 75 | GO:0030851 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | granulocyte differentiation |
| 76 | GO:0030852 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | regulation of granulocyte differentiation |
| 77 | GO:0030853 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of granulocyte differentiation |
| 78 | GO:0002704 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of leukocyte mediated immunity |
| 79 | GO:0002707 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of lymphocyte mediated immunity |
| 80 | GO:0120126 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | response to copper ion starvation |
| 81 | GO:0006067 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | ethanol metabolic process |
| 82 | GO:0006069 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | ethanol oxidation |
| 83 | GO:0009846 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | pollen germination |
| 84 | GO:0002855 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | regulation of natural killer cell mediated immune response to tumor cell |
| 85 | GO:0002856 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of natural killer cell mediated immune response to tumor cell |
| 86 | GO:0002858 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | regulation of natural killer cell mediated cytotoxicity directed against tumor cell target |
| 87 | GO:0002859 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target |
| 88 | GO:0018343 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | protein farnesylation |
| 89 | GO:0002834 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | regulation of response to tumor cell |
| 90 | GO:0002835 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of response to tumor cell |
| 91 | GO:0002837 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | regulation of immune response to tumor cell |
| 92 | GO:0002838 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of immune response to tumor cell |
| 93 | GO:0051055 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of lipid biosynthetic process |
| 94 | GO:0051023 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | regulation of immunoglobulin secretion |
| 95 | GO:0051024 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | positive regulation of immunoglobulin secretion |
| 96 | GO:0035726 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | common myeloid progenitor cell proliferation |
| 97 | GO:1900047 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of hemostasis |
| 98 | GO:0035874 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | cellular response to copper ion starvation |
| 99 | GO:1901143 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | insulin catabolic process |
| 100 | GO:0034111 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of homotypic cell-cell adhesion |
| 101 | GO:0034104 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of tissue remodeling |
| 102 | GO:0045779 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of bone resorption |
| 103 | GO:0044342 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | type B pancreatic cell proliferation |
| 104 | GO:0045887 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | positive regulation of synaptic growth at neuromuscular junction |
| 105 | GO:0055069 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | zinc ion homeostasis |
| 106 | GO:0061469 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | regulation of type B pancreatic cell proliferation |
| 107 | GO:0032703 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation of interleukin-2 production |
| 108 | GO:0044793 | 0.0166006 | Inf | 0.0166006 | 1 | 1 | negative regulation by host of viral process |
| 109 | GO:0044091 | 0.0188719 | 10.997886 | 0.2158083 | 2 | 13 | membrane biogenesis |
| 110 | GO:0060548 | 0.0210832 | 3.390706 | 1.5936616 | 5 | 96 | negative regulation of cell death |
| 111 | GO:0007009 | 0.0217823 | 10.079457 | 0.2324090 | 2 | 14 | plasma membrane organization |
| 112 | GO:0055076 | 0.0217823 | 10.079457 | 0.2324090 | 2 | 14 | transition metal ion homeostasis |
| 113 | GO:0042594 | 0.0262791 | 5.075490 | 0.6474250 | 3 | 39 | response to starvation |
| 114 | GO:0008643 | 0.0281153 | 8.636213 | 0.2656103 | 2 | 16 | carbohydrate transport |
| 115 | GO:0007034 | 0.0299384 | 4.806502 | 0.6806263 | 3 | 41 | vacuolar transport |
| 116 | GO:0006310 | 0.0299384 | 4.806502 | 0.6806263 | 3 | 41 | DNA recombination |
| 117 | GO:0044854 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | plasma membrane raft assembly |
| 118 | GO:0044857 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | plasma membrane raft organization |
| 119 | GO:1904313 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | response to methamphetamine hydrochloride |
| 120 | GO:0032663 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | regulation of interleukin-2 production |
| 121 | GO:0032652 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | regulation of interleukin-1 production |
| 122 | GO:0032623 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | interleukin-2 production |
| 123 | GO:0032612 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | interleukin-1 production |
| 124 | GO:0042149 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | cellular response to glucose starvation |
| 125 | GO:0050850 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | positive regulation of calcium-mediated signaling |
| 126 | GO:0050818 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | regulation of coagulation |
| 127 | GO:0042267 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | natural killer cell mediated cytotoxicity |
| 128 | GO:0042269 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | regulation of natural killer cell mediated cytotoxicity |
| 129 | GO:0071353 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | cellular response to interleukin-4 |
| 130 | GO:0071359 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | cellular response to dsRNA |
| 131 | GO:0048340 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | paraxial mesoderm morphogenesis |
| 132 | GO:0070070 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | proton-transporting V-type ATPase complex assembly |
| 133 | GO:0070072 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | vacuolar proton-transporting V-type ATPase complex assembly |
| 134 | GO:0071287 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | cellular response to manganese ion |
| 135 | GO:0010042 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | response to manganese ion |
| 136 | GO:0048867 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | stem cell fate determination |
| 137 | GO:0070231 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | T cell apoptotic process |
| 138 | GO:0070232 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | regulation of T cell apoptotic process |
| 139 | GO:2001185 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | regulation of CD8-positive, alpha-beta T cell activation |
| 140 | GO:2001187 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | positive regulation of CD8-positive, alpha-beta T cell activation |
| 141 | GO:0090324 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | negative regulation of oxidative phosphorylation |
| 142 | GO:0070670 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | response to interleukin-4 |
| 143 | GO:2000345 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | regulation of hepatocyte proliferation |
| 144 | GO:2000346 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | negative regulation of hepatocyte proliferation |
| 145 | GO:0046640 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | regulation of alpha-beta T cell proliferation |
| 146 | GO:0046633 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | alpha-beta T cell proliferation |
| 147 | GO:0021589 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | cerebellum structural organization |
| 148 | GO:0021577 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | hindbrain structural organization |
| 149 | GO:0043331 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | response to dsRNA |
| 150 | GO:0030026 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | cellular manganese ion homeostasis |
| 151 | GO:0019054 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | modulation by virus of host process |
| 152 | GO:0019080 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | viral gene expression |
| 153 | GO:0019083 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | viral transcription |
| 154 | GO:0019048 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | modulation by virus of host morphology or physiology |
| 155 | GO:0090503 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | RNA phosphodiester bond hydrolysis, exonucleolytic |
| 156 | GO:2000561 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | regulation of CD4-positive, alpha-beta T cell proliferation |
| 157 | GO:0030193 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | regulation of blood coagulation |
| 158 | GO:0002228 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | natural killer cell mediated immunity |
| 159 | GO:0002761 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | regulation of myeloid leukocyte differentiation |
| 160 | GO:0002762 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | negative regulation of myeloid leukocyte differentiation |
| 161 | GO:0002715 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | regulation of natural killer cell mediated immunity |
| 162 | GO:0072574 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | hepatocyte proliferation |
| 163 | GO:0072575 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | epithelial cell proliferation involved in liver morphogenesis |
| 164 | GO:0072576 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | liver morphogenesis |
| 165 | GO:0016036 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | cellular response to phosphate starvation |
| 166 | GO:1903894 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | regulation of IRE1-mediated unfolded protein response |
| 167 | GO:0035739 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | CD4-positive, alpha-beta T cell proliferation |
| 168 | GO:1900046 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | regulation of hemostasis |
| 169 | GO:0002637 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | regulation of immunoglobulin production |
| 170 | GO:0002639 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | positive regulation of immunoglobulin production |
| 171 | GO:1901142 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | insulin metabolic process |
| 172 | GO:0044068 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | modulation by symbiont of host cellular process |
| 173 | GO:0016338 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules |
| 174 | GO:0034110 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | regulation of homotypic cell-cell adhesion |
| 175 | GO:0044003 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | modification by symbiont of host morphology or physiology |
| 176 | GO:0061045 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | negative regulation of wound healing |
| 177 | GO:1990090 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | cellular response to nerve growth factor stimulus |
| 178 | GO:1990089 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | response to nerve growth factor |
| 179 | GO:0055071 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | manganese ion homeostasis |
| 180 | GO:0045670 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | regulation of osteoclast differentiation |
| 181 | GO:0045671 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | negative regulation of osteoclast differentiation |
| 182 | GO:0045601 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | regulation of endothelial cell differentiation |
| 183 | GO:1901998 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | toxin transport |
| 184 | GO:0036037 | 0.0329288 | 59.908046 | 0.0332013 | 1 | 2 | CD8-positive, alpha-beta T cell activation |
| 185 | GO:0051962 | 0.0359055 | 4.452224 | 0.7304282 | 3 | 44 | positive regulation of nervous system development |
| 186 | GO:0031032 | 0.0359055 | 4.452224 | 0.7304282 | 3 | 44 | actomyosin structure organization |
| 187 | GO:0010941 | 0.0366111 | 2.594235 | 2.4734956 | 6 | 149 | regulation of cell death |
| 188 | GO:0050678 | 0.0388018 | 7.108071 | 0.3154122 | 2 | 19 | regulation of epithelial cell proliferation |
| 189 | GO:0045069 | 0.0388018 | 7.108071 | 0.3154122 | 2 | 19 | regulation of viral genome replication |
| 190 | GO:0048524 | 0.0426566 | 6.711886 | 0.3320128 | 2 | 20 | positive regulation of viral process |
| 191 | GO:0006414 | 0.0426566 | 6.711886 | 0.3320128 | 2 | 20 | translational elongation |
| 192 | GO:0071345 | 0.0447408 | 4.053333 | 0.7968308 | 3 | 48 | cellular response to cytokine stimulus |
| 193 | GO:0043066 | 0.0448827 | 3.176252 | 1.3446520 | 4 | 81 | negative regulation of apoptotic process |
| 194 | GO:0034641 | 0.0449812 | 1.489675 | 28.0550840 | 36 | 1690 | cellular nitrogen compound metabolic process |
| 195 | GO:0090501 | 0.0466482 | 6.357405 | 0.3486135 | 2 | 21 | RNA phosphodiester bond hydrolysis |
| 196 | GO:0045980 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | negative regulation of nucleotide metabolic process |
| 197 | GO:0006983 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | ER overload response |
| 198 | GO:0042130 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | negative regulation of T cell proliferation |
| 199 | GO:0042102 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | positive regulation of T cell proliferation |
| 200 | GO:0036335 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | intestinal stem cell homeostasis |
| 201 | GO:0048339 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | paraxial mesoderm development |
| 202 | GO:0070071 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | proton-transporting two-sector ATPase complex assembly |
| 203 | GO:0050672 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | negative regulation of lymphocyte proliferation |
| 204 | GO:0032945 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | negative regulation of mononuclear cell proliferation |
| 205 | GO:0036213 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | contractile ring contraction |
| 206 | GO:0001765 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | membrane raft assembly |
| 207 | GO:0048532 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | anatomical structure arrangement |
| 208 | GO:0000212 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | meiotic spindle organization |
| 209 | GO:0070664 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | negative regulation of leukocyte proliferation |
| 210 | GO:0002082 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | regulation of oxidative phosphorylation |
| 211 | GO:0043114 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | regulation of vascular permeability |
| 212 | GO:0043116 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | negative regulation of vascular permeability |
| 213 | GO:0000959 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | mitochondrial RNA metabolic process |
| 214 | GO:0000916 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | actomyosin contractile ring contraction |
| 215 | GO:1903035 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | negative regulation of response to wounding |
| 216 | GO:0110111 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | negative regulation of animal organ morphogenesis |
| 217 | GO:0002377 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | immunoglobulin production |
| 218 | GO:2000516 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | positive regulation of CD4-positive, alpha-beta T cell activation |
| 219 | GO:0031579 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | membrane raft organization |
| 220 | GO:0035455 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | response to interferon-alpha |
| 221 | GO:0035437 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | maintenance of protein localization in endoplasmic reticulum |
| 222 | GO:0009856 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | pollination |
| 223 | GO:1903579 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | negative regulation of ATP metabolic process |
| 224 | GO:0045453 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | bone resorption |
| 225 | GO:0045124 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | regulation of bone resorption |
| 226 | GO:1900101 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | regulation of endoplasmic reticulum unfolded protein response |
| 227 | GO:0055092 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | sterol homeostasis |
| 228 | GO:1900543 | 0.0489888 | 29.948276 | 0.0498019 | 1 | 3 | negative regulation of purine nucleotide metabolic process |
Module 7
GO_term_black <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_black.csv")
GO_term_black %>%
kbl() %>%
kable_styling(bootstrap_options = "striped", full_width = F, position = "left") %>%
kable_paper() %>%
scroll_box(width = "800px", height = "200px")| X | GOBPID | Pvalue | OddsRatio | ExpCount | Count | Size | Term |
|---|---|---|---|---|---|---|---|
| 1 | GO:0051127 | 0.0000000 | 193.308823 | 0.0662139 | 5 | 9 | positive regulation of actin nucleation |
| 2 | GO:0051125 | 0.0000000 | 154.617647 | 0.0735710 | 5 | 10 | regulation of actin nucleation |
| 3 | GO:0006030 | 0.0000000 | 30.891047 | 0.3237125 | 7 | 44 | chitin metabolic process |
| 4 | GO:1901071 | 0.0000000 | 27.855945 | 0.3531409 | 7 | 48 | glucosamine-containing compound metabolic process |
| 5 | GO:0006040 | 0.0000000 | 27.187500 | 0.3604980 | 7 | 49 | amino sugar metabolic process |
| 6 | GO:0006022 | 0.0000001 | 24.804348 | 0.3899264 | 7 | 53 | aminoglycan metabolic process |
| 7 | GO:0042752 | 0.0000002 | 51.441176 | 0.1471420 | 5 | 20 | regulation of circadian rhythm |
| 8 | GO:0045010 | 0.0000004 | 45.371972 | 0.1618563 | 5 | 22 | actin nucleation |
| 9 | GO:0030838 | 0.0000008 | 38.544118 | 0.1839276 | 5 | 25 | positive regulation of actin filament polymerization |
| 10 | GO:0007623 | 0.0000029 | 28.513072 | 0.2354273 | 5 | 32 | circadian rhythm |
| 11 | GO:0030833 | 0.0000039 | 26.536511 | 0.2501415 | 5 | 34 | regulation of actin filament polymerization |
| 12 | GO:0030041 | 0.0000046 | 25.647059 | 0.2574986 | 5 | 35 | actin filament polymerization |
| 13 | GO:0008064 | 0.0000053 | 24.814991 | 0.2648557 | 5 | 36 | regulation of actin polymerization or depolymerization |
| 14 | GO:0030832 | 0.0000053 | 24.814991 | 0.2648557 | 5 | 36 | regulation of actin filament length |
| 15 | GO:0032273 | 0.0000079 | 22.612457 | 0.2869270 | 5 | 39 | positive regulation of protein polymerization |
| 16 | GO:0008154 | 0.0000090 | 21.962185 | 0.2942841 | 5 | 40 | actin polymerization or depolymerization |
| 17 | GO:0110053 | 0.0000115 | 20.767091 | 0.3089983 | 5 | 42 | regulation of actin filament organization |
| 18 | GO:0031334 | 0.0000146 | 19.694570 | 0.3237125 | 5 | 44 | positive regulation of protein complex assembly |
| 19 | GO:1902905 | 0.0000163 | 19.198529 | 0.3310696 | 5 | 45 | positive regulation of supramolecular fiber organization |
| 20 | GO:0051495 | 0.0000225 | 17.848837 | 0.3531409 | 5 | 48 | positive regulation of cytoskeleton organization |
| 21 | GO:0032271 | 0.0000225 | 17.848837 | 0.3531409 | 5 | 48 | regulation of protein polymerization |
| 22 | GO:0032956 | 0.0000249 | 17.439840 | 0.3604980 | 5 | 49 | regulation of actin cytoskeleton organization |
| 23 | GO:0048511 | 0.0000275 | 17.049020 | 0.3678551 | 5 | 50 | rhythmic process |
| 24 | GO:0032535 | 0.0000440 | 15.329412 | 0.4046406 | 5 | 55 | regulation of cellular component size |
| 25 | GO:0043254 | 0.0000524 | 14.734163 | 0.4193548 | 5 | 57 | regulation of protein complex assembly |
| 26 | GO:0051258 | 0.0000672 | 13.922460 | 0.4414261 | 5 | 60 | protein polymerization |
| 27 | GO:0032970 | 0.0000729 | 13.671219 | 0.4487832 | 5 | 61 | regulation of actin filament-based process |
| 28 | GO:1902903 | 0.0000852 | 13.194726 | 0.4634975 | 5 | 63 | regulation of supramolecular fiber organization |
| 29 | GO:0007015 | 0.0000919 | 12.968594 | 0.4708546 | 5 | 64 | actin filament organization |
| 30 | GO:0090066 | 0.0001065 | 12.538573 | 0.4855688 | 5 | 66 | regulation of anatomical structure size |
| 31 | GO:0051493 | 0.0001412 | 11.757919 | 0.5149972 | 5 | 70 | regulation of cytoskeleton organization |
| 32 | GO:0044089 | 0.0002220 | 10.600490 | 0.5664969 | 5 | 77 | positive regulation of cellular component biogenesis |
| 33 | GO:0017144 | 0.0002469 | 6.592271 | 1.2948500 | 7 | 176 | drug metabolic process |
| 34 | GO:0010638 | 0.0006506 | 8.264067 | 0.7136389 | 5 | 97 | positive regulation of organelle organization |
| 35 | GO:0008152 | 0.0009875 | 4.337692 | 26.1397849 | 35 | 3553 | metabolic process |
| 36 | GO:0006629 | 0.0010122 | 4.557309 | 2.1335597 | 8 | 290 | lipid metabolic process |
| 37 | GO:0097435 | 0.0016386 | 6.640867 | 0.8754952 | 5 | 119 | supramolecular fiber organization |
| 38 | GO:0044087 | 0.0021852 | 6.195757 | 0.9343520 | 5 | 127 | regulation of cellular component biogenesis |
| 39 | GO:1901135 | 0.0022360 | 3.985484 | 2.4131296 | 8 | 328 | carbohydrate derivative metabolic process |
| 40 | GO:0030036 | 0.0022619 | 6.144189 | 0.9417091 | 5 | 128 | actin cytoskeleton organization |
| 41 | GO:0030029 | 0.0023405 | 6.093453 | 0.9490662 | 5 | 129 | actin filament-based process |
| 42 | GO:0045892 | 0.0023405 | 6.093453 | 0.9490662 | 5 | 129 | negative regulation of transcription, DNA-templated |
| 43 | GO:1902679 | 0.0025038 | 5.994398 | 0.9637804 | 5 | 131 | negative regulation of RNA biosynthetic process |
| 44 | GO:1903507 | 0.0025038 | 5.994398 | 0.9637804 | 5 | 131 | negative regulation of nucleic acid-templated transcription |
| 45 | GO:0051253 | 0.0025884 | 5.946040 | 0.9711375 | 5 | 132 | negative regulation of RNA metabolic process |
| 46 | GO:2000113 | 0.0033428 | 5.584967 | 1.0299943 | 5 | 140 | negative regulation of cellular macromolecule biosynthetic process |
| 47 | GO:0045934 | 0.0035539 | 5.501288 | 1.0447085 | 5 | 142 | negative regulation of nucleobase-containing compound metabolic process |
| 48 | GO:0007010 | 0.0036576 | 4.578019 | 1.5229202 | 6 | 207 | cytoskeleton organization |
| 49 | GO:0010558 | 0.0037745 | 5.420017 | 1.0594228 | 5 | 144 | negative regulation of macromolecule biosynthetic process |
| 50 | GO:0031327 | 0.0042451 | 5.264295 | 1.0888512 | 5 | 148 | negative regulation of cellular biosynthetic process |
| 51 | GO:0009890 | 0.0046247 | 5.153102 | 1.1109225 | 5 | 151 | negative regulation of biosynthetic process |
| 52 | GO:0051130 | 0.0047564 | 5.117047 | 1.1182796 | 5 | 152 | positive regulation of cellular component organization |
| 53 | GO:0006869 | 0.0063447 | 8.865646 | 0.3825693 | 3 | 52 | lipid transport |
| 54 | GO:0033043 | 0.0074284 | 4.571377 | 1.2433503 | 5 | 169 | regulation of organelle organization |
| 55 | GO:0010876 | 0.0107844 | 7.225000 | 0.4634975 | 3 | 63 | lipid localization |
| 56 | GO:0034622 | 0.0120041 | 4.035771 | 1.3978495 | 5 | 190 | cellular protein-containing complex assembly |
| 57 | GO:0010629 | 0.0141661 | 3.862389 | 1.4567063 | 5 | 198 | negative regulation of gene expression |
| 58 | GO:0090210 | 0.0146615 | 138.447368 | 0.0147142 | 1 | 2 | regulation of establishment of blood-brain barrier |
| 59 | GO:0090212 | 0.0146615 | 138.447368 | 0.0147142 | 1 | 2 | negative regulation of establishment of blood-brain barrier |
| 60 | GO:0051452 | 0.0146615 | 138.447368 | 0.0147142 | 1 | 2 | intracellular pH reduction |
| 61 | GO:0045851 | 0.0146615 | 138.447368 | 0.0147142 | 1 | 2 | pH reduction |
| 62 | GO:0042360 | 0.0146615 | 138.447368 | 0.0147142 | 1 | 2 | vitamin E metabolic process |
| 63 | GO:0050912 | 0.0219134 | 69.210526 | 0.0220713 | 1 | 3 | detection of chemical stimulus involved in sensory perception of taste |
| 64 | GO:0050907 | 0.0219134 | 69.210526 | 0.0220713 | 1 | 3 | detection of chemical stimulus involved in sensory perception |
| 65 | GO:0035337 | 0.0219134 | 69.210526 | 0.0220713 | 1 | 3 | fatty-acyl-CoA metabolic process |
| 66 | GO:0009593 | 0.0219134 | 69.210526 | 0.0220713 | 1 | 3 | detection of chemical stimulus |
| 67 | GO:0051180 | 0.0219134 | 69.210526 | 0.0220713 | 1 | 3 | vitamin transport |
| 68 | GO:0051172 | 0.0241893 | 3.338633 | 1.6700623 | 5 | 227 | negative regulation of nitrogen compound metabolic process |
| 69 | GO:0065003 | 0.0280504 | 3.202827 | 1.7362762 | 5 | 236 | protein-containing complex assembly |
| 70 | GO:0031324 | 0.0280504 | 3.202827 | 1.7362762 | 5 | 236 | negative regulation of cellular metabolic process |
| 71 | GO:0060856 | 0.0291134 | 46.131579 | 0.0294284 | 1 | 4 | establishment of blood-brain barrier |
| 72 | GO:0051453 | 0.0291134 | 46.131579 | 0.0294284 | 1 | 4 | regulation of intracellular pH |
| 73 | GO:0065008 | 0.0312557 | 2.568326 | 3.0899830 | 7 | 420 | regulation of biological quality |
| 74 | GO:0030004 | 0.0362617 | 34.592105 | 0.0367855 | 1 | 5 | cellular monovalent inorganic cation homeostasis |
| 75 | GO:0120009 | 0.0362617 | 34.592105 | 0.0367855 | 1 | 5 | intermembrane lipid transfer |
| 76 | GO:0030641 | 0.0362617 | 34.592105 | 0.0367855 | 1 | 5 | regulation of cellular pH |
| 77 | GO:0071704 | 0.0369178 | 1.998812 | 23.1307301 | 29 | 3144 | organic substance metabolic process |
| 78 | GO:0000209 | 0.0394076 | 6.883322 | 0.3163554 | 2 | 43 | protein polyubiquitination |
| 79 | GO:0009268 | 0.0433587 | 27.668421 | 0.0441426 | 1 | 6 | response to pH |
| 80 | GO:0043933 | 0.0461176 | 2.773030 | 1.9864177 | 5 | 270 | protein-containing complex subunit organization |
| 81 | GO:0010605 | 0.0498979 | 2.708379 | 2.0305603 | 5 | 276 | negative regulation of macromolecule metabolic process |
Module 9
GO_term_magenta <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_magenta.csv")
GO_term_magenta %>%
kbl() %>%
kable_styling(bootstrap_options = "striped", full_width = F, position = "left") %>%
kable_paper() %>%
scroll_box(width = "800px", height = "200px")| X | GOBPID | Pvalue | OddsRatio | ExpCount | Count | Size | Term |
|---|---|---|---|---|---|---|---|
| 1 | GO:0046034 | 0.0000000 | 75.565217 | 0.4708546 | 16 | 64 | ATP metabolic process |
| 2 | GO:0009205 | 0.0000000 | 71.079284 | 0.4929259 | 16 | 67 | purine ribonucleoside triphosphate metabolic process |
| 3 | GO:0009199 | 0.0000000 | 69.698997 | 0.5002830 | 16 | 68 | ribonucleoside triphosphate metabolic process |
| 4 | GO:0009144 | 0.0000000 | 68.370796 | 0.5076401 | 16 | 69 | purine nucleoside triphosphate metabolic process |
| 5 | GO:0009167 | 0.0000000 | 64.670807 | 0.5297114 | 16 | 72 | purine ribonucleoside monophosphate metabolic process |
| 6 | GO:0009126 | 0.0000000 | 64.670807 | 0.5297114 | 16 | 72 | purine nucleoside monophosphate metabolic process |
| 7 | GO:0009141 | 0.0000000 | 63.524028 | 0.5370685 | 16 | 73 | nucleoside triphosphate metabolic process |
| 8 | GO:0009161 | 0.0000000 | 61.347089 | 0.5517827 | 16 | 75 | ribonucleoside monophosphate metabolic process |
| 9 | GO:0009123 | 0.0000000 | 60.313043 | 0.5591398 | 16 | 76 | nucleoside monophosphate metabolic process |
| 10 | GO:0009150 | 0.0000000 | 42.369309 | 0.7430673 | 16 | 101 | purine ribonucleotide metabolic process |
| 11 | GO:0009259 | 0.0000000 | 41.379310 | 0.7577816 | 16 | 103 | ribonucleotide metabolic process |
| 12 | GO:0006163 | 0.0000000 | 39.529861 | 0.7872100 | 16 | 107 | purine nucleotide metabolic process |
| 13 | GO:0019693 | 0.0000000 | 39.092628 | 0.7945671 | 16 | 108 | ribose phosphate metabolic process |
| 14 | GO:0072521 | 0.0000000 | 36.279315 | 0.8460668 | 16 | 115 | purine-containing compound metabolic process |
| 15 | GO:0017144 | 0.0000000 | 27.688969 | 1.2948500 | 18 | 176 | drug metabolic process |
| 16 | GO:0009117 | 0.0000000 | 27.035573 | 1.0888512 | 16 | 148 | nucleotide metabolic process |
| 17 | GO:0006753 | 0.0000000 | 26.419324 | 1.1109225 | 16 | 151 | nucleoside phosphate metabolic process |
| 18 | GO:0055086 | 0.0000000 | 21.489328 | 1.3316355 | 16 | 181 | nucleobase-containing small molecule metabolic process |
| 19 | GO:0006754 | 0.0000000 | 74.871429 | 0.2207131 | 9 | 30 | ATP biosynthetic process |
| 20 | GO:0009145 | 0.0000000 | 68.334783 | 0.2354273 | 9 | 32 | purine nucleoside triphosphate biosynthetic process |
| 21 | GO:0009206 | 0.0000000 | 68.334783 | 0.2354273 | 9 | 32 | purine ribonucleoside triphosphate biosynthetic process |
| 22 | GO:0009142 | 0.0000000 | 65.475000 | 0.2427844 | 9 | 33 | nucleoside triphosphate biosynthetic process |
| 23 | GO:0009201 | 0.0000000 | 65.475000 | 0.2427844 | 9 | 33 | ribonucleoside triphosphate biosynthetic process |
| 24 | GO:0019637 | 0.0000000 | 15.689179 | 1.9422750 | 17 | 264 | organophosphate metabolic process |
| 25 | GO:0022904 | 0.0000000 | 96.737327 | 0.1618563 | 8 | 22 | respiratory electron transport chain |
| 26 | GO:0006119 | 0.0000000 | 90.270968 | 0.1692134 | 8 | 23 | oxidative phosphorylation |
| 27 | GO:0015985 | 0.0000000 | 164.218750 | 0.1029994 | 7 | 14 | energy coupled proton transport, down electrochemical gradient |
| 28 | GO:0015986 | 0.0000000 | 164.218750 | 0.1029994 | 7 | 14 | ATP synthesis coupled proton transport |
| 29 | GO:0009168 | 0.0000000 | 56.078571 | 0.2722128 | 9 | 37 | purine ribonucleoside monophosphate biosynthetic process |
| 30 | GO:0009127 | 0.0000000 | 56.078571 | 0.2722128 | 9 | 37 | purine nucleoside monophosphate biosynthetic process |
| 31 | GO:0009156 | 0.0000000 | 52.320000 | 0.2869270 | 9 | 39 | ribonucleoside monophosphate biosynthetic process |
| 32 | GO:0009124 | 0.0000000 | 50.622581 | 0.2942841 | 9 | 40 | nucleoside monophosphate biosynthetic process |
| 33 | GO:0022900 | 0.0000000 | 71.212224 | 0.1986418 | 8 | 27 | electron transport chain |
| 34 | GO:0045333 | 0.0000000 | 46.129412 | 0.3163554 | 9 | 43 | cellular respiration |
| 35 | GO:1901135 | 0.0000000 | 12.301520 | 2.4131296 | 17 | 328 | carbohydrate derivative metabolic process |
| 36 | GO:0042773 | 0.0000000 | 95.703125 | 0.1397849 | 7 | 19 | ATP synthesis coupled electron transport |
| 37 | GO:0006091 | 0.0000000 | 29.400791 | 0.5223543 | 10 | 71 | generation of precursor metabolites and energy |
| 38 | GO:0015980 | 0.0000000 | 36.411628 | 0.3825693 | 9 | 52 | energy derivation by oxidation of organic compounds |
| 39 | GO:0009152 | 0.0000000 | 32.587500 | 0.4193548 | 9 | 57 | purine ribonucleotide biosynthetic process |
| 40 | GO:0046390 | 0.0000000 | 31.272000 | 0.4340690 | 9 | 59 | ribose phosphate biosynthetic process |
| 41 | GO:0009260 | 0.0000000 | 31.272000 | 0.4340690 | 9 | 59 | ribonucleotide biosynthetic process |
| 42 | GO:0006164 | 0.0000000 | 30.652941 | 0.4414261 | 9 | 60 | purine nucleotide biosynthetic process |
| 43 | GO:0072522 | 0.0000000 | 28.933333 | 0.4634975 | 9 | 63 | purine-containing compound biosynthetic process |
| 44 | GO:0044281 | 0.0000000 | 9.535220 | 3.3254103 | 18 | 452 | small molecule metabolic process |
| 45 | GO:0042775 | 0.0000000 | 106.121212 | 0.1103565 | 6 | 15 | mitochondrial ATP synthesis coupled electron transport |
| 46 | GO:1902600 | 0.0000000 | 47.742188 | 0.2280702 | 7 | 31 | proton transmembrane transport |
| 47 | GO:0009165 | 0.0000000 | 20.748000 | 0.6179966 | 9 | 84 | nucleotide biosynthetic process |
| 48 | GO:1901293 | 0.0000000 | 20.748000 | 0.6179966 | 9 | 84 | nucleoside phosphate biosynthetic process |
| 49 | GO:0090407 | 0.0000000 | 13.506186 | 1.0373514 | 10 | 141 | organophosphate biosynthetic process |
| 50 | GO:0055114 | 0.0000001 | 8.667247 | 2.2071307 | 13 | 300 | oxidation-reduction process |
| 51 | GO:0098662 | 0.0000001 | 17.847742 | 0.6106395 | 8 | 83 | inorganic cation transmembrane transport |
| 52 | GO:0098660 | 0.0000001 | 17.151365 | 0.6327108 | 8 | 86 | inorganic ion transmembrane transport |
| 53 | GO:0098655 | 0.0000005 | 14.188058 | 0.7504244 | 8 | 102 | cation transmembrane transport |
| 54 | GO:1901137 | 0.0000006 | 10.023645 | 1.3610640 | 10 | 185 | carbohydrate derivative biosynthetic process |
| 55 | GO:0006796 | 0.0000008 | 5.549513 | 5.3118280 | 18 | 722 | phosphate-containing compound metabolic process |
| 56 | GO:0006793 | 0.0000009 | 5.504332 | 5.3486135 | 18 | 727 | phosphorus metabolic process |
| 57 | GO:0015672 | 0.0000060 | 12.292799 | 0.7283531 | 7 | 99 | monovalent inorganic cation transport |
| 58 | GO:0034220 | 0.0000219 | 8.282410 | 1.2286361 | 8 | 167 | ion transmembrane transport |
| 59 | GO:0006120 | 0.0000300 | 73.000000 | 0.0662139 | 3 | 9 | mitochondrial electron transport, NADH to ubiquinone |
| 60 | GO:0006812 | 0.0001248 | 6.366011 | 1.5670628 | 8 | 213 | cation transport |
| 61 | GO:0006122 | 0.0001575 | 284.378378 | 0.0220713 | 2 | 3 | mitochondrial electron transport, ubiquinol to cytochrome c |
| 62 | GO:1901566 | 0.0008748 | 3.708759 | 3.7889078 | 11 | 515 | organonitrogen compound biosynthetic process |
| 63 | GO:0006811 | 0.0030153 | 3.783410 | 2.5308432 | 8 | 344 | ion transport |
| 64 | GO:0032981 | 0.0039090 | 25.803440 | 0.0956423 | 2 | 13 | mitochondrial respiratory chain complex I assembly |
| 65 | GO:0010257 | 0.0039090 | 25.803440 | 0.0956423 | 2 | 13 | NADH dehydrogenase complex assembly |
| 66 | GO:0055085 | 0.0047344 | 3.247416 | 3.3401245 | 9 | 454 | transmembrane transport |
| 67 | GO:0007005 | 0.0047444 | 6.567619 | 0.6915676 | 4 | 94 | mitochondrion organization |
| 68 | GO:0033108 | 0.0066904 | 18.908108 | 0.1250707 | 2 | 17 | mitochondrial respiratory chain complex assembly |
| 69 | GO:0006139 | 0.0072839 | 2.353025 | 10.4691568 | 18 | 1423 | nucleobase-containing compound metabolic process |
| 70 | GO:1902957 | 0.0073571 | Inf | 0.0073571 | 1 | 1 | negative regulation of mitochondrial electron transport, NADH to ubiquinone |
| 71 | GO:0006123 | 0.0073571 | Inf | 0.0073571 | 1 | 1 | mitochondrial electron transport, cytochrome c to oxygen |
| 72 | GO:1901856 | 0.0073571 | Inf | 0.0073571 | 1 | 1 | negative regulation of cellular respiration |
| 73 | GO:1905447 | 0.0073571 | Inf | 0.0073571 | 1 | 1 | negative regulation of mitochondrial ATP synthesis coupled electron transport |
| 74 | GO:0009060 | 0.0101412 | 14.916074 | 0.1544992 | 2 | 21 | aerobic respiration |
| 75 | GO:0046483 | 0.0102690 | 2.253399 | 10.8002264 | 18 | 1468 | heterocycle metabolic process |
| 76 | GO:0006725 | 0.0103454 | 2.251255 | 10.8075835 | 18 | 1469 | cellular aromatic compound metabolic process |
| 77 | GO:1901564 | 0.0129385 | 2.162080 | 12.8234295 | 20 | 1743 | organonitrogen compound metabolic process |
| 78 | GO:1901360 | 0.0137145 | 2.169894 | 11.0945105 | 18 | 1508 | organic cyclic compound metabolic process |
| 79 | GO:0090324 | 0.0146615 | 138.447368 | 0.0147142 | 1 | 2 | negative regulation of oxidative phosphorylation |
| 80 | GO:1902956 | 0.0146615 | 138.447368 | 0.0147142 | 1 | 2 | regulation of mitochondrial electron transport, NADH to ubiquinone |
| 81 | GO:0019646 | 0.0146615 | 138.447368 | 0.0147142 | 1 | 2 | aerobic electron transport chain |
| 82 | GO:1905446 | 0.0146615 | 138.447368 | 0.0147142 | 1 | 2 | regulation of mitochondrial ATP synthesis coupled electron transport |
| 83 | GO:0032780 | 0.0146615 | 138.447368 | 0.0147142 | 1 | 2 | negative regulation of ATPase activity |
| 84 | GO:0016310 | 0.0160223 | 2.773042 | 3.3548387 | 8 | 456 | phosphorylation |
| 85 | GO:0034641 | 0.0205583 | 2.041562 | 12.4335031 | 19 | 1690 | cellular nitrogen compound metabolic process |
| 86 | GO:0006936 | 0.0214425 | 9.753961 | 0.2280702 | 2 | 31 | muscle contraction |
| 87 | GO:0045980 | 0.0219134 | 69.210526 | 0.0220713 | 1 | 3 | negative regulation of nucleotide metabolic process |
| 88 | GO:0002082 | 0.0219134 | 69.210526 | 0.0220713 | 1 | 3 | regulation of oxidative phosphorylation |
| 89 | GO:2000983 | 0.0219134 | 69.210526 | 0.0220713 | 1 | 3 | regulation of ATP citrate synthase activity |
| 90 | GO:2000984 | 0.0219134 | 69.210526 | 0.0220713 | 1 | 3 | negative regulation of ATP citrate synthase activity |
| 91 | GO:1903579 | 0.0219134 | 69.210526 | 0.0220713 | 1 | 3 | negative regulation of ATP metabolic process |
| 92 | GO:0055070 | 0.0219134 | 69.210526 | 0.0220713 | 1 | 3 | copper ion homeostasis |
| 93 | GO:0006662 | 0.0219134 | 69.210526 | 0.0220713 | 1 | 3 | glycerol ether metabolic process |
| 94 | GO:0018904 | 0.0219134 | 69.210526 | 0.0220713 | 1 | 3 | ether metabolic process |
| 95 | GO:1900543 | 0.0219134 | 69.210526 | 0.0220713 | 1 | 3 | negative regulation of purine nucleotide metabolic process |
| 96 | GO:0030150 | 0.0291134 | 46.131579 | 0.0294284 | 1 | 4 | protein import into mitochondrial matrix |
| 97 | GO:0035434 | 0.0291134 | 46.131579 | 0.0294284 | 1 | 4 | copper ion transmembrane transport |
| 98 | GO:0003012 | 0.0345109 | 7.431010 | 0.2942841 | 2 | 40 | muscle system process |
| 99 | GO:0062014 | 0.0362617 | 34.592105 | 0.0367855 | 1 | 5 | negative regulation of small molecule metabolic process |
| 100 | GO:0043457 | 0.0362617 | 34.592105 | 0.0367855 | 1 | 5 | regulation of cellular respiration |
| 101 | GO:1900037 | 0.0362617 | 34.592105 | 0.0367855 | 1 | 5 | regulation of cellular response to hypoxia |
| 102 | GO:0006825 | 0.0362617 | 34.592105 | 0.0367855 | 1 | 5 | copper ion transport |
| 103 | GO:0048793 | 0.0433587 | 27.668421 | 0.0441426 | 1 | 6 | pronephros development |
| 104 | GO:0055065 | 0.0463204 | 6.266667 | 0.3457838 | 2 | 47 | metal ion homeostasis |
| 105 | GO:0044057 | 0.0481140 | 6.129260 | 0.3531409 | 2 | 48 | regulation of system process |
Module 10
GO_term_purple <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_purple.csv")
GO_term_purple %>%
kbl() %>%
kable_styling(bootstrap_options = "striped", full_width = F, position = "left") %>%
kable_paper() %>%
scroll_box(width = "800px", height = "200px")| X | GOBPID | Pvalue | OddsRatio | ExpCount | Count | Size | Term |
|---|---|---|---|---|---|---|---|
| 1 | GO:0070527 | 0.0000000 | 101.389961 | 0.0950764 | 5 | 12 | platelet aggregation |
| 2 | GO:0030168 | 0.0000000 | 88.699324 | 0.1029994 | 5 | 13 | platelet activation |
| 3 | GO:0034109 | 0.0000000 | 88.699324 | 0.1029994 | 5 | 13 | homotypic cell-cell adhesion |
| 4 | GO:0050817 | 0.0000001 | 64.471744 | 0.1267685 | 5 | 16 | coagulation |
| 5 | GO:0007596 | 0.0000001 | 64.471744 | 0.1267685 | 5 | 16 | blood coagulation |
| 6 | GO:0007599 | 0.0000001 | 64.471744 | 0.1267685 | 5 | 16 | hemostasis |
| 7 | GO:0009612 | 0.0000001 | 33.544872 | 0.2535371 | 6 | 32 | response to mechanical stimulus |
| 8 | GO:0030029 | 0.0000005 | 11.679545 | 1.0220713 | 9 | 129 | actin filament-based process |
| 9 | GO:0050878 | 0.0000006 | 41.669316 | 0.1743067 | 5 | 22 | regulation of body fluid levels |
| 10 | GO:0030036 | 0.0000055 | 10.076471 | 1.0141483 | 8 | 128 | actin cytoskeleton organization |
| 11 | GO:0098974 | 0.0000091 | 134.769231 | 0.0475382 | 3 | 6 | postsynaptic actin cytoskeleton organization |
| 12 | GO:0099188 | 0.0000091 | 134.769231 | 0.0475382 | 3 | 6 | postsynaptic cytoskeleton organization |
| 13 | GO:0035902 | 0.0000091 | 134.769231 | 0.0475382 | 3 | 6 | response to immobilization stress |
| 14 | GO:0071257 | 0.0000158 | 101.057692 | 0.0554612 | 3 | 7 | cellular response to electrical stimulus |
| 15 | GO:0002121 | 0.0000158 | 101.057692 | 0.0554612 | 3 | 7 | inter-male aggressive behavior |
| 16 | GO:1903920 | 0.0000158 | 101.057692 | 0.0554612 | 3 | 7 | positive regulation of actin filament severing |
| 17 | GO:1903919 | 0.0000158 | 101.057692 | 0.0554612 | 3 | 7 | negative regulation of actin filament severing |
| 18 | GO:0035995 | 0.0000158 | 101.057692 | 0.0554612 | 3 | 7 | detection of muscle stretch |
| 19 | GO:0055003 | 0.0000158 | 101.057692 | 0.0554612 | 3 | 7 | cardiac myofibril assembly |
| 20 | GO:1904030 | 0.0000158 | 101.057692 | 0.0554612 | 3 | 7 | negative regulation of cyclin-dependent protein kinase activity |
| 21 | GO:0048857 | 0.0000252 | 80.830769 | 0.0633843 | 3 | 8 | neural nucleus development |
| 22 | GO:0021762 | 0.0000252 | 80.830769 | 0.0633843 | 3 | 8 | substantia nigra development |
| 23 | GO:0002118 | 0.0000252 | 80.830769 | 0.0633843 | 3 | 8 | aggressive behavior |
| 24 | GO:0016319 | 0.0000252 | 80.830769 | 0.0633843 | 3 | 8 | mushroom body development |
| 25 | GO:1903918 | 0.0000252 | 80.830769 | 0.0633843 | 3 | 8 | regulation of actin filament severing |
| 26 | GO:0045663 | 0.0000252 | 80.830769 | 0.0633843 | 3 | 8 | positive regulation of myoblast differentiation |
| 27 | GO:0042060 | 0.0000293 | 16.785714 | 0.3723826 | 5 | 47 | wound healing |
| 28 | GO:0007291 | 0.0000376 | 67.346154 | 0.0713073 | 3 | 9 | sperm individualization |
| 29 | GO:0010831 | 0.0000376 | 67.346154 | 0.0713073 | 3 | 9 | positive regulation of myotube differentiation |
| 30 | GO:0014897 | 0.0000376 | 67.346154 | 0.0713073 | 3 | 9 | striated muscle hypertrophy |
| 31 | GO:0051014 | 0.0000376 | 67.346154 | 0.0713073 | 3 | 9 | actin filament severing |
| 32 | GO:0035994 | 0.0000376 | 67.346154 | 0.0713073 | 3 | 9 | response to muscle stretch |
| 33 | GO:0055013 | 0.0000376 | 67.346154 | 0.0713073 | 3 | 9 | cardiac muscle cell development |
| 34 | GO:0045662 | 0.0000376 | 67.346154 | 0.0713073 | 3 | 9 | negative regulation of myoblast differentiation |
| 35 | GO:0003300 | 0.0000376 | 67.346154 | 0.0713073 | 3 | 9 | cardiac muscle hypertrophy |
| 36 | GO:0051091 | 0.0000382 | 26.255639 | 0.1980758 | 4 | 25 | positive regulation of DNA-binding transcription factor activity |
| 37 | GO:0043044 | 0.0000534 | 57.714286 | 0.0792303 | 3 | 10 | ATP-dependent chromatin remodeling |
| 38 | GO:0090175 | 0.0000534 | 57.714286 | 0.0792303 | 3 | 10 | regulation of establishment of planar polarity |
| 39 | GO:0002026 | 0.0000534 | 57.714286 | 0.0792303 | 3 | 10 | regulation of the force of heart contraction |
| 40 | GO:0014896 | 0.0000534 | 57.714286 | 0.0792303 | 3 | 10 | muscle hypertrophy |
| 41 | GO:0030901 | 0.0000534 | 57.714286 | 0.0792303 | 3 | 10 | midbrain development |
| 42 | GO:0050982 | 0.0000730 | 50.490385 | 0.0871534 | 3 | 11 | detection of mechanical stimulus |
| 43 | GO:0007349 | 0.0000730 | 50.490385 | 0.0871534 | 3 | 11 | cellularization |
| 44 | GO:0010830 | 0.0000730 | 50.490385 | 0.0871534 | 3 | 11 | regulation of myotube differentiation |
| 45 | GO:0051155 | 0.0000730 | 50.490385 | 0.0871534 | 3 | 11 | positive regulation of striated muscle cell differentiation |
| 46 | GO:0051149 | 0.0000730 | 50.490385 | 0.0871534 | 3 | 11 | positive regulation of muscle cell differentiation |
| 47 | GO:0055006 | 0.0000730 | 50.490385 | 0.0871534 | 3 | 11 | cardiac cell development |
| 48 | GO:0060048 | 0.0000730 | 50.490385 | 0.0871534 | 3 | 11 | cardiac muscle contraction |
| 49 | GO:0009611 | 0.0000755 | 13.531705 | 0.4516129 | 5 | 57 | response to wounding |
| 50 | GO:0006874 | 0.0000804 | 21.186235 | 0.2376910 | 4 | 30 | cellular calcium ion homeostasis |
| 51 | GO:0006936 | 0.0000918 | 20.397661 | 0.2456140 | 4 | 31 | muscle contraction |
| 52 | GO:0072503 | 0.0000918 | 20.397661 | 0.2456140 | 4 | 31 | cellular divalent inorganic cation homeostasis |
| 53 | GO:0001974 | 0.0000968 | 44.871795 | 0.0950764 | 3 | 12 | blood vessel remodeling |
| 54 | GO:0032091 | 0.0000968 | 44.871795 | 0.0950764 | 3 | 12 | negative regulation of protein binding |
| 55 | GO:0051602 | 0.0000968 | 44.871795 | 0.0950764 | 3 | 12 | response to electrical stimulus |
| 56 | GO:0051090 | 0.0001043 | 19.665413 | 0.2535371 | 4 | 32 | regulation of DNA-binding transcription factor activity |
| 57 | GO:0055074 | 0.0001043 | 19.665413 | 0.2535371 | 4 | 32 | calcium ion homeostasis |
| 58 | GO:0042592 | 0.0001127 | 6.417457 | 1.5370685 | 8 | 194 | homeostatic process |
| 59 | GO:0001775 | 0.0001224 | 12.117894 | 0.4991511 | 5 | 63 | cell activation |
| 60 | GO:0032507 | 0.0001252 | 40.376923 | 0.1029994 | 3 | 13 | maintenance of protein location in cell |
| 61 | GO:0051651 | 0.0001252 | 40.376923 | 0.1029994 | 3 | 13 | maintenance of location in cell |
| 62 | GO:0072507 | 0.0001492 | 17.752122 | 0.2773062 | 4 | 35 | divalent inorganic cation homeostasis |
| 63 | GO:0006941 | 0.0001585 | 36.699301 | 0.1109225 | 3 | 14 | striated muscle contraction |
| 64 | GO:0045445 | 0.0001585 | 36.699301 | 0.1109225 | 3 | 14 | myoblast differentiation |
| 65 | GO:0051153 | 0.0001585 | 36.699301 | 0.1109225 | 3 | 14 | regulation of striated muscle cell differentiation |
| 66 | GO:0045661 | 0.0001585 | 36.699301 | 0.1109225 | 3 | 14 | regulation of myoblast differentiation |
| 67 | GO:0007010 | 0.0001771 | 5.982856 | 1.6400679 | 8 | 207 | cytoskeleton organization |
| 68 | GO:0052646 | 0.0001829 | 262.900000 | 0.0237691 | 2 | 3 | alditol phosphate metabolic process |
| 69 | GO:0006072 | 0.0001829 | 262.900000 | 0.0237691 | 2 | 3 | glycerol-3-phosphate metabolic process |
| 70 | GO:0001895 | 0.0001970 | 33.634615 | 0.1188455 | 3 | 15 | retina homeostasis |
| 71 | GO:0045214 | 0.0001970 | 33.634615 | 0.1188455 | 3 | 15 | sarcomere organization |
| 72 | GO:0051147 | 0.0001970 | 33.634615 | 0.1188455 | 3 | 15 | regulation of muscle cell differentiation |
| 73 | GO:0055007 | 0.0001970 | 33.634615 | 0.1188455 | 3 | 15 | cardiac muscle cell differentiation |
| 74 | GO:0000281 | 0.0002411 | 31.041420 | 0.1267685 | 3 | 16 | mitotic cytokinesis |
| 75 | GO:0014902 | 0.0002411 | 31.041420 | 0.1267685 | 3 | 16 | myotube differentiation |
| 76 | GO:0045185 | 0.0002411 | 31.041420 | 0.1267685 | 3 | 16 | maintenance of protein location |
| 77 | GO:0051100 | 0.0002411 | 31.041420 | 0.1267685 | 3 | 16 | negative regulation of binding |
| 78 | GO:1904029 | 0.0002411 | 31.041420 | 0.1267685 | 3 | 16 | regulation of cyclin-dependent protein kinase activity |
| 79 | GO:0003012 | 0.0002531 | 15.271930 | 0.3169213 | 4 | 40 | muscle system process |
| 80 | GO:0006811 | 0.0002629 | 4.607972 | 2.7255235 | 10 | 344 | ion transport |
| 81 | GO:0006875 | 0.0002788 | 14.856330 | 0.3248444 | 4 | 41 | cellular metal ion homeostasis |
| 82 | GO:0051705 | 0.0002912 | 28.818681 | 0.1346916 | 3 | 17 | multi-organism behavior |
| 83 | GO:1905330 | 0.0002912 | 28.818681 | 0.1346916 | 3 | 17 | regulation of morphogenesis of an epithelium |
| 84 | GO:0009628 | 0.0003585 | 6.136145 | 1.3706848 | 7 | 173 | response to abiotic stimulus |
| 85 | GO:0031032 | 0.0003674 | 13.734210 | 0.3486135 | 4 | 44 | actomyosin structure organization |
| 86 | GO:0030003 | 0.0004009 | 13.396662 | 0.3565365 | 4 | 45 | cellular cation homeostasis |
| 87 | GO:0006873 | 0.0004009 | 13.396662 | 0.3565365 | 4 | 45 | cellular ion homeostasis |
| 88 | GO:0035051 | 0.0004104 | 25.206731 | 0.1505376 | 3 | 19 | cardiocyte differentiation |
| 89 | GO:0055065 | 0.0004745 | 12.768666 | 0.3723826 | 4 | 47 | metal ion homeostasis |
| 90 | GO:0048771 | 0.0004801 | 23.719457 | 0.1584607 | 3 | 20 | tissue remodeling |
| 91 | GO:0099173 | 0.0004801 | 23.719457 | 0.1584607 | 3 | 20 | postsynapse organization |
| 92 | GO:0044057 | 0.0005147 | 12.476077 | 0.3803056 | 4 | 48 | regulation of system process |
| 93 | GO:0001736 | 0.0005571 | 22.397436 | 0.1663837 | 3 | 21 | establishment of planar polarity |
| 94 | GO:0098609 | 0.0005594 | 8.531641 | 0.6893039 | 5 | 87 | cell-cell adhesion |
| 95 | GO:0055082 | 0.0006022 | 11.929062 | 0.3961517 | 4 | 50 | cellular chemical homeostasis |
| 96 | GO:0061983 | 0.0006037 | 87.600000 | 0.0396152 | 2 | 5 | meiosis II cell cycle process |
| 97 | GO:0007111 | 0.0006037 | 87.600000 | 0.0396152 | 2 | 5 | meiosis II cytokinesis |
| 98 | GO:0033206 | 0.0006037 | 87.600000 | 0.0396152 | 2 | 5 | meiotic cytokinesis |
| 99 | GO:0061640 | 0.0006415 | 21.214575 | 0.1743067 | 3 | 22 | cytoskeleton-dependent cytokinesis |
| 100 | GO:0001738 | 0.0006415 | 21.214575 | 0.1743067 | 3 | 22 | morphogenesis of a polarized epithelium |
| 101 | GO:0007164 | 0.0006415 | 21.214575 | 0.1743067 | 3 | 22 | establishment of tissue polarity |
| 102 | GO:0048646 | 0.0006769 | 6.473485 | 1.0933786 | 6 | 138 | anatomical structure formation involved in morphogenesis |
| 103 | GO:0051179 | 0.0006939 | 2.906479 | 10.0860215 | 20 | 1273 | localization |
| 104 | GO:0035148 | 0.0007337 | 20.150000 | 0.1822298 | 3 | 23 | tube formation |
| 105 | GO:0006469 | 0.0007337 | 20.150000 | 0.1822298 | 3 | 23 | negative regulation of protein kinase activity |
| 106 | GO:0008016 | 0.0008339 | 19.186813 | 0.1901528 | 3 | 24 | regulation of heart contraction |
| 107 | GO:0065009 | 0.0008710 | 4.636406 | 2.0758347 | 8 | 262 | regulation of molecular function |
| 108 | GO:0006796 | 0.0008784 | 3.213983 | 5.7204301 | 14 | 722 | phosphate-containing compound metabolic process |
| 109 | GO:0098771 | 0.0009280 | 10.540486 | 0.4436899 | 4 | 56 | inorganic ion homeostasis |
| 110 | GO:0055080 | 0.0009280 | 10.540486 | 0.4436899 | 4 | 56 | cation homeostasis |
| 111 | GO:0006793 | 0.0009420 | 3.187938 | 5.7600453 | 14 | 727 | phosphorus metabolic process |
| 112 | GO:2000027 | 0.0009424 | 18.311189 | 0.1980758 | 3 | 25 | regulation of animal organ morphogenesis |
| 113 | GO:0043393 | 0.0009424 | 18.311189 | 0.1980758 | 3 | 25 | regulation of protein binding |
| 114 | GO:0003015 | 0.0009424 | 18.311189 | 0.1980758 | 3 | 25 | heart process |
| 115 | GO:0060047 | 0.0009424 | 18.311189 | 0.1980758 | 3 | 25 | heart contraction |
| 116 | GO:0033673 | 0.0010594 | 17.511706 | 0.2059989 | 3 | 26 | negative regulation of kinase activity |
| 117 | GO:0009581 | 0.0010594 | 17.511706 | 0.2059989 | 3 | 26 | detection of external stimulus |
| 118 | GO:0009582 | 0.0010594 | 17.511706 | 0.2059989 | 3 | 26 | detection of abiotic stimulus |
| 119 | GO:0009653 | 0.0010895 | 4.073554 | 2.6859083 | 9 | 339 | anatomical structure morphogenesis |
| 120 | GO:0019725 | 0.0011053 | 7.267736 | 0.8002264 | 5 | 101 | cellular homeostasis |
| 121 | GO:0030239 | 0.0011853 | 16.778846 | 0.2139219 | 3 | 27 | myofibril assembly |
| 122 | GO:1903522 | 0.0011853 | 16.778846 | 0.2139219 | 3 | 27 | regulation of blood circulation |
| 123 | GO:0032970 | 0.0012813 | 9.606648 | 0.4833050 | 4 | 61 | regulation of actin filament-based process |
| 124 | GO:0048738 | 0.0013203 | 16.104615 | 0.2218449 | 3 | 28 | cardiac muscle tissue development |
| 125 | GO:0032989 | 0.0014207 | 5.562092 | 1.2597623 | 6 | 159 | cellular component morphogenesis |
| 126 | GO:0050801 | 0.0014459 | 9.277431 | 0.4991511 | 4 | 63 | ion homeostasis |
| 127 | GO:0000910 | 0.0014645 | 15.482249 | 0.2297680 | 3 | 29 | cytokinesis |
| 128 | GO:0006338 | 0.0014645 | 15.482249 | 0.2297680 | 3 | 29 | chromatin remodeling |
| 129 | GO:0051348 | 0.0016183 | 14.905983 | 0.2376910 | 3 | 30 | negative regulation of transferase activity |
| 130 | GO:0043086 | 0.0017197 | 8.823429 | 0.5229202 | 4 | 66 | negative regulation of catalytic activity |
| 131 | GO:0071214 | 0.0017819 | 14.370879 | 0.2456140 | 3 | 31 | cellular response to abiotic stimulus |
| 132 | GO:0001894 | 0.0017819 | 14.370879 | 0.2456140 | 3 | 31 | tissue homeostasis |
| 133 | GO:0007519 | 0.0017819 | 14.370879 | 0.2456140 | 3 | 31 | skeletal muscle tissue development |
| 134 | GO:0104004 | 0.0017819 | 14.370879 | 0.2456140 | 3 | 31 | cellular response to environmental stimulus |
| 135 | GO:0034220 | 0.0018282 | 5.277433 | 1.3231466 | 6 | 167 | ion transmembrane transport |
| 136 | GO:0007623 | 0.0019554 | 13.872679 | 0.2535371 | 3 | 32 | circadian rhythm |
| 137 | GO:0051606 | 0.0019554 | 13.872679 | 0.2535371 | 3 | 32 | detection of stimulus |
| 138 | GO:0060538 | 0.0021392 | 13.407692 | 0.2614601 | 3 | 33 | skeletal muscle organ development |
| 139 | GO:0008015 | 0.0021392 | 13.407692 | 0.2614601 | 3 | 33 | blood circulation |
| 140 | GO:0003013 | 0.0021392 | 13.407692 | 0.2614601 | 3 | 33 | circulatory system process |
| 141 | GO:0055002 | 0.0021392 | 13.407692 | 0.2614601 | 3 | 33 | striated muscle cell development |
| 142 | GO:0010927 | 0.0023333 | 12.972705 | 0.2693831 | 3 | 34 | cellular component assembly involved in morphogenesis |
| 143 | GO:0051098 | 0.0023333 | 12.972705 | 0.2693831 | 3 | 34 | regulation of binding |
| 144 | GO:0055001 | 0.0023333 | 12.972705 | 0.2693831 | 3 | 34 | muscle cell development |
| 145 | GO:0006909 | 0.0025381 | 12.564904 | 0.2773062 | 3 | 35 | phagocytosis |
| 146 | GO:0048871 | 0.0025381 | 12.564904 | 0.2773062 | 3 | 35 | multicellular organismal homeostasis |
| 147 | GO:0051235 | 0.0025381 | 12.564904 | 0.2773062 | 3 | 35 | maintenance of location |
| 148 | GO:0001523 | 0.0026492 | 32.818750 | 0.0792303 | 2 | 10 | retinoid metabolic process |
| 149 | GO:0016101 | 0.0026492 | 32.818750 | 0.0792303 | 2 | 10 | diterpenoid metabolic process |
| 150 | GO:0007286 | 0.0027536 | 12.181818 | 0.2852292 | 3 | 36 | spermatid development |
| 151 | GO:0048515 | 0.0029802 | 11.821267 | 0.2931522 | 3 | 37 | spermatid differentiation |
| 152 | GO:0046434 | 0.0032179 | 11.481319 | 0.3010753 | 3 | 38 | organophosphate catabolic process |
| 153 | GO:0006721 | 0.0032217 | 29.166667 | 0.0871534 | 2 | 11 | terpenoid metabolic process |
| 154 | GO:0006816 | 0.0034670 | 11.160256 | 0.3089983 | 3 | 39 | calcium ion transport |
| 155 | GO:0045944 | 0.0036436 | 7.084074 | 0.6417657 | 4 | 81 | positive regulation of transcription by RNA polymerase II |
| 156 | GO:0030001 | 0.0039688 | 5.331601 | 1.0696095 | 5 | 135 | metal ion transport |
| 157 | GO:0044092 | 0.0039787 | 6.902065 | 0.6576118 | 4 | 83 | negative regulation of molecular function |
| 158 | GO:0048878 | 0.0043341 | 6.729045 | 0.6734578 | 4 | 85 | chemical homeostasis |
| 159 | GO:0006835 | 0.0045233 | 23.854545 | 0.1029994 | 2 | 13 | dicarboxylic acid transport |
| 160 | GO:0051146 | 0.0045801 | 10.036539 | 0.3406904 | 3 | 43 | striated muscle cell differentiation |
| 161 | GO:0060041 | 0.0045801 | 10.036539 | 0.3406904 | 3 | 43 | retina development in camera-type eye |
| 162 | GO:0065008 | 0.0047661 | 3.216987 | 3.3276740 | 9 | 420 | regulation of biological quality |
| 163 | GO:0001933 | 0.0048883 | 9.789869 | 0.3486135 | 3 | 44 | negative regulation of protein phosphorylation |
| 164 | GO:0009887 | 0.0050734 | 5.014689 | 1.1329938 | 5 | 143 | animal organ morphogenesis |
| 165 | GO:0070838 | 0.0052088 | 9.554945 | 0.3565365 | 3 | 45 | divalent metal ion transport |
| 166 | GO:0072511 | 0.0052088 | 9.554945 | 0.3565365 | 3 | 45 | divalent inorganic cation transport |
| 167 | GO:0030866 | 0.0052507 | 21.862500 | 0.1109225 | 2 | 14 | cortical actin cytoskeleton organization |
| 168 | GO:0015849 | 0.0055418 | 9.330948 | 0.3644595 | 3 | 46 | organic acid transport |
| 169 | GO:0046942 | 0.0055418 | 9.330948 | 0.3644595 | 3 | 46 | carboxylic acid transport |
| 170 | GO:0007155 | 0.0057009 | 4.869623 | 1.1646859 | 5 | 147 | cell adhesion |
| 171 | GO:0022610 | 0.0057009 | 4.869623 | 1.1646859 | 5 | 147 | biological adhesion |
| 172 | GO:0042692 | 0.0058873 | 9.117133 | 0.3723826 | 3 | 47 | muscle cell differentiation |
| 173 | GO:0030865 | 0.0060282 | 20.176923 | 0.1188455 | 2 | 15 | cortical cytoskeleton organization |
| 174 | GO:0050808 | 0.0062454 | 8.912821 | 0.3803056 | 3 | 48 | synapse organization |
| 175 | GO:0060249 | 0.0070003 | 8.530278 | 0.3961517 | 3 | 50 | anatomical structure homeostasis |
| 176 | GO:0048511 | 0.0070003 | 8.530278 | 0.3961517 | 3 | 50 | rhythmic process |
| 177 | GO:0042326 | 0.0073972 | 8.350962 | 0.4040747 | 3 | 51 | negative regulation of phosphorylation |
| 178 | GO:0150063 | 0.0074394 | 5.721884 | 0.7843803 | 4 | 99 | visual system development |
| 179 | GO:0048880 | 0.0074394 | 5.721884 | 0.7843803 | 4 | 99 | sensory system development |
| 180 | GO:0001654 | 0.0074394 | 5.721884 | 0.7843803 | 4 | 99 | eye development |
| 181 | GO:0055085 | 0.0079173 | 2.950357 | 3.5970572 | 9 | 454 | transmembrane transport |
| 182 | GO:0046168 | 0.0079230 | Inf | 0.0079230 | 1 | 1 | glycerol-3-phosphate catabolic process |
| 183 | GO:0035025 | 0.0079230 | Inf | 0.0079230 | 1 | 1 | positive regulation of Rho protein signal transduction |
| 184 | GO:0006002 | 0.0079230 | Inf | 0.0079230 | 1 | 1 | fructose 6-phosphate metabolic process |
| 185 | GO:0016310 | 0.0081434 | 2.935936 | 3.6129032 | 9 | 456 | phosphorylation |
| 186 | GO:0009605 | 0.0083069 | 3.799397 | 1.7985286 | 6 | 227 | response to external stimulus |
| 187 | GO:0045859 | 0.0086671 | 7.855204 | 0.4278438 | 3 | 54 | regulation of protein kinase activity |
| 188 | GO:0034613 | 0.0087466 | 3.365424 | 2.3927561 | 7 | 302 | cellular protein localization |
| 189 | GO:0051301 | 0.0091171 | 7.702663 | 0.4357668 | 3 | 55 | cell division |
| 190 | GO:0006468 | 0.0092346 | 3.064471 | 3.0345218 | 8 | 383 | protein phosphorylation |
| 191 | GO:0070727 | 0.0093757 | 3.317726 | 2.4244482 | 7 | 306 | cellular macromolecule localization |
| 192 | GO:0048513 | 0.0095183 | 3.046965 | 3.0503679 | 8 | 385 | animal organ development |
| 193 | GO:0014706 | 0.0095807 | 7.555878 | 0.4436899 | 3 | 56 | striated muscle tissue development |
| 194 | GO:0015711 | 0.0100578 | 7.414530 | 0.4516129 | 3 | 57 | organic anion transport |
| 195 | GO:0060537 | 0.0110531 | 7.146978 | 0.4674590 | 3 | 59 | muscle tissue development |
| 196 | GO:0045936 | 0.0115715 | 7.020243 | 0.4753820 | 3 | 60 | negative regulation of phosphate metabolic process |
| 197 | GO:0007517 | 0.0115715 | 7.020243 | 0.4753820 | 3 | 60 | muscle organ development |
| 198 | GO:0010563 | 0.0115715 | 7.020243 | 0.4753820 | 3 | 60 | negative regulation of phosphorus metabolic process |
| 199 | GO:0043549 | 0.0115715 | 7.020243 | 0.4753820 | 3 | 60 | regulation of kinase activity |
| 200 | GO:1903508 | 0.0117498 | 4.973443 | 0.8953028 | 4 | 113 | positive regulation of nucleic acid-templated transcription |
| 201 | GO:0045893 | 0.0117498 | 4.973443 | 0.8953028 | 4 | 113 | positive regulation of transcription, DNA-templated |
| 202 | GO:0007283 | 0.0121038 | 6.897878 | 0.4833050 | 3 | 61 | spermatogenesis |
| 203 | GO:1902680 | 0.0121080 | 4.927273 | 0.9032258 | 4 | 114 | positive regulation of RNA biosynthetic process |
| 204 | GO:0043010 | 0.0126500 | 6.779661 | 0.4912281 | 3 | 62 | camera-type eye development |
| 205 | GO:0007423 | 0.0136112 | 4.750693 | 0.9349179 | 4 | 118 | sensory organ development |
| 206 | GO:0007409 | 0.0137844 | 6.554855 | 0.5070741 | 3 | 64 | axonogenesis |
| 207 | GO:0009166 | 0.0139552 | 12.471429 | 0.1822298 | 2 | 23 | nucleotide catabolic process |
| 208 | GO:0003333 | 0.0139552 | 12.471429 | 0.1822298 | 2 | 23 | amino acid transmembrane transport |
| 209 | GO:0097435 | 0.0140048 | 4.708467 | 0.9428410 | 4 | 119 | supramolecular fiber organization |
| 210 | GO:0033365 | 0.0148138 | 4.626181 | 0.9586870 | 4 | 121 | protein localization to organelle |
| 211 | GO:0048232 | 0.0149753 | 6.344322 | 0.5229202 | 3 | 66 | male gamete generation |
| 212 | GO:0000060 | 0.0157848 | 128.243902 | 0.0158461 | 1 | 2 | protein import into nucleus, translocation |
| 213 | GO:0031288 | 0.0157848 | 128.243902 | 0.0158461 | 1 | 2 | sorocarp morphogenesis |
| 214 | GO:0045596 | 0.0162230 | 6.146746 | 0.5387663 | 3 | 68 | negative regulation of cell differentiation |
| 215 | GO:1901292 | 0.0163834 | 11.382609 | 0.1980758 | 2 | 25 | nucleoside phosphate catabolic process |
| 216 | GO:0006865 | 0.0163834 | 11.382609 | 0.1980758 | 2 | 25 | amino acid transport |
| 217 | GO:0010557 | 0.0165196 | 4.469769 | 0.9903792 | 4 | 125 | positive regulation of macromolecule biosynthetic process |
| 218 | GO:0006810 | 0.0173709 | 2.142198 | 8.6994907 | 15 | 1098 | transport |
| 219 | GO:0031400 | 0.0182017 | 5.872172 | 0.5625354 | 3 | 71 | negative regulation of protein modification process |
| 220 | GO:0031328 | 0.0193032 | 4.253626 | 1.0379174 | 4 | 131 | positive regulation of cellular biosynthetic process |
| 221 | GO:0051254 | 0.0197938 | 4.219572 | 1.0458404 | 4 | 132 | positive regulation of RNA metabolic process |
| 222 | GO:0003006 | 0.0202921 | 4.186046 | 1.0537634 | 4 | 133 | developmental process involved in reproduction |
| 223 | GO:0035023 | 0.0203367 | 10.063462 | 0.2218449 | 2 | 28 | regulation of Rho protein signal transduction |
| 224 | GO:1903825 | 0.0203367 | 10.063462 | 0.2218449 | 2 | 28 | organic acid transmembrane transport |
| 225 | GO:1905039 | 0.0203367 | 10.063462 | 0.2218449 | 2 | 28 | carboxylic acid transmembrane transport |
| 226 | GO:0051338 | 0.0210411 | 5.541667 | 0.5942275 | 3 | 75 | regulation of transferase activity |
| 227 | GO:0006720 | 0.0217346 | 9.688889 | 0.2297680 | 2 | 29 | isoprenoid metabolic process |
| 228 | GO:0061564 | 0.0217870 | 5.464700 | 0.6021505 | 3 | 76 | axon development |
| 229 | GO:0048667 | 0.0217870 | 5.464700 | 0.6021505 | 3 | 76 | cell morphogenesis involved in neuron differentiation |
| 230 | GO:0007281 | 0.0217870 | 5.464700 | 0.6021505 | 3 | 76 | germ cell development |
| 231 | GO:0006897 | 0.0217870 | 5.464700 | 0.6021505 | 3 | 76 | endocytosis |
| 232 | GO:0051234 | 0.0221567 | 2.067125 | 8.9451047 | 15 | 1129 | establishment of localization |
| 233 | GO:0009891 | 0.0223633 | 4.056985 | 1.0854556 | 4 | 137 | positive regulation of biosynthetic process |
| 234 | GO:0007507 | 0.0225473 | 5.389813 | 0.6100736 | 3 | 77 | heart development |
| 235 | GO:0032975 | 0.0235857 | 64.109756 | 0.0237691 | 1 | 3 | amino acid transmembrane import into vacuole |
| 236 | GO:0046579 | 0.0235857 | 64.109756 | 0.0237691 | 1 | 3 | positive regulation of Ras protein signal transduction |
| 237 | GO:0015802 | 0.0235857 | 64.109756 | 0.0237691 | 1 | 3 | basic amino acid transport |
| 238 | GO:0051057 | 0.0235857 | 64.109756 | 0.0237691 | 1 | 3 | positive regulation of small GTPase mediated signal transduction |
| 239 | GO:0034486 | 0.0235857 | 64.109756 | 0.0237691 | 1 | 3 | vacuolar transmembrane transport |
| 240 | GO:0006820 | 0.0241113 | 5.245951 | 0.6259196 | 3 | 79 | anion transport |
| 241 | GO:0048468 | 0.0241985 | 2.952550 | 2.2739106 | 6 | 287 | cell development |
| 242 | GO:0007266 | 0.0246466 | 9.017241 | 0.2456140 | 2 | 31 | Rho protein signal transduction |
| 243 | GO:0032502 | 0.0247864 | 2.219088 | 5.8313526 | 11 | 736 | developmental process |
| 244 | GO:0006812 | 0.0253625 | 3.281575 | 1.6876061 | 5 | 213 | cation transport |
| 245 | GO:0022603 | 0.0257332 | 5.109468 | 0.6417657 | 3 | 81 | regulation of anatomical structure morphogenesis |
| 246 | GO:1903046 | 0.0261594 | 8.715000 | 0.2535371 | 2 | 32 | meiotic cell cycle process |
| 247 | GO:0045935 | 0.0268851 | 3.820829 | 1.1488398 | 4 | 145 | positive regulation of nucleobase-containing compound metabolic process |
| 248 | GO:0022412 | 0.0274128 | 4.979808 | 0.6576118 | 3 | 83 | cellular process involved in reproduction in multicellular organism |
| 249 | GO:0045597 | 0.0274128 | 4.979808 | 0.6576118 | 3 | 83 | positive regulation of cell differentiation |
| 250 | GO:0098657 | 0.0274128 | 4.979808 | 0.6576118 | 3 | 83 | import into cell |
| 251 | GO:0034404 | 0.0277091 | 8.432258 | 0.2614601 | 2 | 33 | nucleobase-containing small molecule biosynthetic process |
| 252 | GO:0048858 | 0.0291501 | 4.856473 | 0.6734578 | 3 | 85 | cell projection morphogenesis |
| 253 | GO:0048812 | 0.0291501 | 4.856473 | 0.6734578 | 3 | 85 | neuron projection morphogenesis |
| 254 | GO:0002009 | 0.0291501 | 4.856473 | 0.6734578 | 3 | 85 | morphogenesis of an epithelium |
| 255 | GO:0120039 | 0.0291501 | 4.856473 | 0.6734578 | 3 | 85 | plasma membrane bounded cell projection morphogenesis |
| 256 | GO:0051093 | 0.0291501 | 4.856473 | 0.6734578 | 3 | 85 | negative regulation of developmental process |
| 257 | GO:0044093 | 0.0293389 | 3.712523 | 1.1805320 | 4 | 149 | positive regulation of molecular function |
| 258 | GO:0008104 | 0.0297878 | 2.582540 | 3.0503679 | 7 | 385 | protein localization |
| 259 | GO:0035239 | 0.0300403 | 4.797034 | 0.6813809 | 3 | 86 | tube morphogenesis |
| 260 | GO:0015729 | 0.0313262 | 42.731707 | 0.0316921 | 1 | 4 | oxaloacetate transport |
| 261 | GO:0010628 | 0.0325896 | 3.585263 | 1.2201471 | 4 | 154 | positive regulation of gene expression |
| 262 | GO:0048856 | 0.0326248 | 2.181335 | 5.3005093 | 10 | 669 | anatomical structure development |
| 263 | GO:0032990 | 0.0337449 | 4.572944 | 0.7130730 | 3 | 90 | cell part morphogenesis |
| 264 | GO:0051321 | 0.0342644 | 7.462857 | 0.2931522 | 2 | 37 | meiotic cell cycle |
| 265 | GO:0098656 | 0.0342644 | 7.462857 | 0.2931522 | 2 | 37 | anion transmembrane transport |
| 266 | GO:0048729 | 0.0386968 | 4.320234 | 0.7526882 | 3 | 95 | tissue morphogenesis |
| 267 | GO:0043090 | 0.0390069 | 32.042683 | 0.0396152 | 1 | 5 | amino acid import |
| 268 | GO:0046578 | 0.0395377 | 6.869737 | 0.3169213 | 2 | 40 | regulation of Ras protein signal transduction |
| 269 | GO:0030154 | 0.0396081 | 2.416418 | 3.2405207 | 7 | 409 | cell differentiation |
| 270 | GO:0000904 | 0.0397296 | 4.272953 | 0.7606112 | 3 | 96 | cell morphogenesis involved in differentiation |
| 271 | GO:0040011 | 0.0427890 | 3.270218 | 1.3310696 | 4 | 168 | locomotion |
| 272 | GO:0007610 | 0.0429124 | 4.137019 | 0.7843803 | 3 | 99 | behavior |
| 273 | GO:0007420 | 0.0440013 | 4.093577 | 0.7923033 | 3 | 100 | brain development |
| 274 | GO:0061061 | 0.0451041 | 4.051020 | 0.8002264 | 3 | 101 | muscle structure development |
| 275 | GO:0003008 | 0.0451865 | 3.209581 | 1.3548387 | 4 | 171 | system process |
| 276 | GO:0050896 | 0.0452893 | 1.827112 | 10.6247878 | 16 | 1341 | response to stimulus |
| 277 | GO:0032269 | 0.0462207 | 4.009324 | 0.8081494 | 3 | 102 | negative regulation of cellular protein metabolic process |
| 278 | GO:0098655 | 0.0462207 | 4.009324 | 0.8081494 | 3 | 102 | cation transmembrane transport |
| 279 | GO:0015740 | 0.0466280 | 25.629268 | 0.0475382 | 1 | 6 | C4-dicarboxylate transport |
| 280 | GO:0015804 | 0.0466280 | 25.629268 | 0.0475382 | 1 | 6 | neutral amino acid transport |
| 281 | GO:0009642 | 0.0466280 | 25.629268 | 0.0475382 | 1 | 6 | response to light intensity |
| 282 | GO:0048869 | 0.0472384 | 2.316268 | 3.3672892 | 7 | 425 | cellular developmental process |
| 283 | GO:0060322 | 0.0473511 | 3.968462 | 0.8160724 | 3 | 103 | head development |
| 284 | GO:0048731 | 0.0488350 | 2.176815 | 4.1279004 | 8 | 521 | system development |
| 285 | GO:0072359 | 0.0496530 | 3.889140 | 0.8319185 | 3 | 105 | circulatory system development |
| 286 | GO:0035295 | 0.0496530 | 3.889140 | 0.8319185 | 3 | 105 | tube development |
Module 13
GO_term_salmon <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_salmon.csv")
GO_term_salmon %>%
kbl() %>%
kable_styling(bootstrap_options = "striped", full_width = F, position = "left") %>%
kable_paper() %>%
scroll_box(width = "800px", height = "200px")| X | GOBPID | Pvalue | OddsRatio | ExpCount | Count | Size | Term |
|---|---|---|---|---|---|---|---|
| 1 | GO:0055114 | 0.0000000 | 37.504152 | 1.5846067 | 19 | 300 | oxidation-reduction process |
| 2 | GO:0006091 | 0.0000000 | 66.279661 | 0.3750236 | 12 | 71 | generation of precursor metabolites and energy |
| 3 | GO:0006099 | 0.0000000 | 263.250000 | 0.0845124 | 8 | 16 | tricarboxylic acid cycle |
| 4 | GO:0006101 | 0.0000000 | 233.955556 | 0.0897944 | 8 | 17 | citrate metabolic process |
| 5 | GO:0072350 | 0.0000000 | 191.345454 | 0.1003584 | 8 | 19 | tricarboxylic acid metabolic process |
| 6 | GO:0009060 | 0.0000000 | 161.846154 | 0.1109225 | 8 | 21 | aerobic respiration |
| 7 | GO:0016999 | 0.0000000 | 131.425000 | 0.1267685 | 8 | 24 | antibiotic metabolic process |
| 8 | GO:0045333 | 0.0000000 | 72.989164 | 0.2271270 | 9 | 43 | cellular respiration |
| 9 | GO:0015980 | 0.0000000 | 57.613219 | 0.2746652 | 9 | 52 | energy derivation by oxidation of organic compounds |
| 10 | GO:0017144 | 0.0000000 | 20.031372 | 0.9296359 | 11 | 176 | drug metabolic process |
| 11 | GO:0019752 | 0.0000000 | 14.701968 | 1.0669685 | 10 | 202 | carboxylic acid metabolic process |
| 12 | GO:0043436 | 0.0000000 | 14.544674 | 1.0775325 | 10 | 204 | oxoacid metabolic process |
| 13 | GO:0006082 | 0.0000000 | 14.544674 | 1.0775325 | 10 | 204 | organic acid metabolic process |
| 14 | GO:0044281 | 0.0000001 | 9.543204 | 2.3874741 | 13 | 452 | small molecule metabolic process |
| 15 | GO:0032981 | 0.0000364 | 63.156000 | 0.0686663 | 3 | 13 | mitochondrial respiratory chain complex I assembly |
| 16 | GO:0010257 | 0.0000364 | 63.156000 | 0.0686663 | 3 | 13 | NADH dehydrogenase complex assembly |
| 17 | GO:0033108 | 0.0000854 | 45.077143 | 0.0897944 | 3 | 17 | mitochondrial respiratory chain complex assembly |
| 18 | GO:0022900 | 0.0003547 | 26.245000 | 0.1426146 | 3 | 27 | electron transport chain |
| 19 | GO:0065002 | 0.0034844 | 26.964103 | 0.0897944 | 2 | 17 | intracellular protein transmembrane transport |
| 20 | GO:0006090 | 0.0034844 | 26.964103 | 0.0897944 | 2 | 17 | pyruvate metabolic process |
| 21 | GO:0016052 | 0.0039071 | 25.274038 | 0.0950764 | 2 | 18 | carbohydrate catabolic process |
| 22 | GO:0046034 | 0.0044337 | 10.253115 | 0.3380494 | 3 | 64 | ATP metabolic process |
| 23 | GO:0009205 | 0.0050442 | 9.766875 | 0.3538955 | 3 | 67 | purine ribonucleoside triphosphate metabolic process |
| 24 | GO:0009199 | 0.0052585 | 9.614769 | 0.3591775 | 3 | 68 | ribonucleoside triphosphate metabolic process |
| 25 | GO:0060317 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | cardiac epithelial to mesenchymal transition |
| 26 | GO:0051930 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | regulation of sensory perception of pain |
| 27 | GO:0071787 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | endoplasmic reticulum tubular network formation |
| 28 | GO:0048755 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | branching morphogenesis of a nerve |
| 29 | GO:0070571 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | negative regulation of neuron projection regeneration |
| 30 | GO:0021801 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | cerebral cortex radial glia guided migration |
| 31 | GO:0021553 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | olfactory nerve development |
| 32 | GO:2000172 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | regulation of branching morphogenesis of a nerve |
| 33 | GO:0033598 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | mammary gland epithelial cell proliferation |
| 34 | GO:0033599 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | regulation of mammary gland epithelial cell proliferation |
| 35 | GO:0033601 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | positive regulation of mammary gland epithelial cell proliferation |
| 36 | GO:0033603 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | positive regulation of dopamine secretion |
| 37 | GO:0033605 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | positive regulation of catecholamine secretion |
| 38 | GO:0022030 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | telencephalon glial cell migration |
| 39 | GO:0008347 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | glial cell migration |
| 40 | GO:0006007 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | glucose catabolic process |
| 41 | GO:1901475 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | pyruvate transmembrane transport |
| 42 | GO:0006850 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | mitochondrial pyruvate transmembrane transport |
| 43 | GO:0006848 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | pyruvate transport |
| 44 | GO:0045687 | 0.0052820 | Inf | 0.0052820 | 1 | 1 | positive regulation of glial cell differentiation |
| 45 | GO:1990542 | 0.0053105 | 21.271255 | 0.1109225 | 2 | 21 | mitochondrial transmembrane transport |
| 46 | GO:0009144 | 0.0054782 | 9.467273 | 0.3644595 | 3 | 69 | purine nucleoside triphosphate metabolic process |
| 47 | GO:0009167 | 0.0061702 | 9.050435 | 0.3803056 | 3 | 72 | purine ribonucleoside monophosphate metabolic process |
| 48 | GO:0009126 | 0.0061702 | 9.050435 | 0.3803056 | 3 | 72 | purine nucleoside monophosphate metabolic process |
| 49 | GO:0009141 | 0.0064120 | 8.919429 | 0.3855876 | 3 | 73 | nucleoside triphosphate metabolic process |
| 50 | GO:0008152 | 0.0066579 | 4.121788 | 18.7670251 | 25 | 3553 | metabolic process |
| 51 | GO:0030308 | 0.0069117 | 18.360140 | 0.1267685 | 2 | 24 | negative regulation of cell growth |
| 52 | GO:0009161 | 0.0069126 | 8.668333 | 0.3961517 | 3 | 75 | ribonucleoside monophosphate metabolic process |
| 53 | GO:0009123 | 0.0071714 | 8.547945 | 0.4014337 | 3 | 76 | nucleoside monophosphate metabolic process |
| 54 | GO:0071806 | 0.0100030 | 14.945869 | 0.1531786 | 2 | 29 | protein transmembrane transport |
| 55 | GO:0051954 | 0.0105371 | 195.259259 | 0.0105640 | 1 | 2 | positive regulation of amine transport |
| 56 | GO:0051931 | 0.0105371 | 195.259259 | 0.0105640 | 1 | 2 | regulation of sensory perception |
| 57 | GO:0046365 | 0.0105371 | 195.259259 | 0.0105640 | 1 | 2 | monosaccharide catabolic process |
| 58 | GO:0021795 | 0.0105371 | 195.259259 | 0.0105640 | 1 | 2 | cerebral cortex cell migration |
| 59 | GO:0021799 | 0.0105371 | 195.259259 | 0.0105640 | 1 | 2 | cerebral cortex radially oriented cell migration |
| 60 | GO:0021885 | 0.0105371 | 195.259259 | 0.0105640 | 1 | 2 | forebrain cell migration |
| 61 | GO:0021545 | 0.0105371 | 195.259259 | 0.0105640 | 1 | 2 | cranial nerve development |
| 62 | GO:0019320 | 0.0105371 | 195.259259 | 0.0105640 | 1 | 2 | hexose catabolic process |
| 63 | GO:0022029 | 0.0105371 | 195.259259 | 0.0105640 | 1 | 2 | telencephalon cell migration |
| 64 | GO:0045685 | 0.0105371 | 195.259259 | 0.0105640 | 1 | 2 | regulation of glial cell differentiation |
| 65 | GO:0006754 | 0.0106827 | 14.409341 | 0.1584607 | 2 | 30 | ATP biosynthetic process |
| 66 | GO:0045926 | 0.0113824 | 13.909814 | 0.1637427 | 2 | 31 | negative regulation of growth |
| 67 | GO:0009145 | 0.0121018 | 13.443590 | 0.1690247 | 2 | 32 | purine nucleoside triphosphate biosynthetic process |
| 68 | GO:0009206 | 0.0121018 | 13.443590 | 0.1690247 | 2 | 32 | purine ribonucleoside triphosphate biosynthetic process |
| 69 | GO:0007005 | 0.0128352 | 6.833407 | 0.4965101 | 3 | 94 | mitochondrion organization |
| 70 | GO:0009142 | 0.0128408 | 13.007444 | 0.1743067 | 2 | 33 | nucleoside triphosphate biosynthetic process |
| 71 | GO:0009201 | 0.0128408 | 13.007444 | 0.1743067 | 2 | 33 | ribonucleoside triphosphate biosynthetic process |
| 72 | GO:0009150 | 0.0155699 | 6.336735 | 0.5334842 | 3 | 101 | purine ribonucleotide metabolic process |
| 73 | GO:2001025 | 0.0157655 | 97.611111 | 0.0158461 | 1 | 3 | positive regulation of response to drug |
| 74 | GO:0014059 | 0.0157655 | 97.611111 | 0.0158461 | 1 | 3 | regulation of dopamine secretion |
| 75 | GO:0014046 | 0.0157655 | 97.611111 | 0.0158461 | 1 | 3 | dopamine secretion |
| 76 | GO:0006108 | 0.0157655 | 97.611111 | 0.0158461 | 1 | 3 | malate metabolic process |
| 77 | GO:0050432 | 0.0157655 | 97.611111 | 0.0158461 | 1 | 3 | catecholamine secretion |
| 78 | GO:0050433 | 0.0157655 | 97.611111 | 0.0158461 | 1 | 3 | regulation of catecholamine secretion |
| 79 | GO:0061180 | 0.0157655 | 97.611111 | 0.0158461 | 1 | 3 | mammary gland epithelium development |
| 80 | GO:0009168 | 0.0159879 | 11.512088 | 0.1954348 | 2 | 37 | purine ribonucleoside monophosphate biosynthetic process |
| 81 | GO:0009127 | 0.0159879 | 11.512088 | 0.1954348 | 2 | 37 | purine nucleoside monophosphate biosynthetic process |
| 82 | GO:0009259 | 0.0164074 | 6.207600 | 0.5440483 | 3 | 103 | ribonucleotide metabolic process |
| 83 | GO:0001558 | 0.0176733 | 10.885655 | 0.2059989 | 2 | 39 | regulation of cell growth |
| 84 | GO:0009156 | 0.0176733 | 10.885655 | 0.2059989 | 2 | 39 | ribonucleoside monophosphate biosynthetic process |
| 85 | GO:0006163 | 0.0181579 | 5.964231 | 0.5651764 | 3 | 107 | purine nucleotide metabolic process |
| 86 | GO:0009124 | 0.0185433 | 10.597166 | 0.2112809 | 2 | 40 | nucleoside monophosphate biosynthetic process |
| 87 | GO:0019693 | 0.0186113 | 5.906286 | 0.5704584 | 3 | 108 | ribose phosphate metabolic process |
| 88 | GO:0051937 | 0.0209672 | 65.061728 | 0.0211281 | 1 | 4 | catecholamine transport |
| 89 | GO:0014015 | 0.0209672 | 65.061728 | 0.0211281 | 1 | 4 | positive regulation of gliogenesis |
| 90 | GO:0021675 | 0.0209672 | 65.061728 | 0.0211281 | 1 | 4 | nerve development |
| 91 | GO:0015872 | 0.0209672 | 65.061728 | 0.0211281 | 1 | 4 | dopamine transport |
| 92 | GO:0043280 | 0.0209672 | 65.061728 | 0.0211281 | 1 | 4 | positive regulation of cysteine-type endopeptidase activity involved in apoptotic process |
| 93 | GO:0030517 | 0.0209672 | 65.061728 | 0.0211281 | 1 | 4 | negative regulation of axon extension |
| 94 | GO:0072521 | 0.0219628 | 5.529643 | 0.6074326 | 3 | 115 | purine-containing compound metabolic process |
| 95 | GO:0051952 | 0.0261423 | 48.787037 | 0.0264101 | 1 | 5 | regulation of amine transport |
| 96 | GO:0071300 | 0.0261423 | 48.787037 | 0.0264101 | 1 | 5 | cellular response to retinoic acid |
| 97 | GO:0071786 | 0.0261423 | 48.787037 | 0.0264101 | 1 | 5 | endoplasmic reticulum tubular network organization |
| 98 | GO:0015837 | 0.0261423 | 48.787037 | 0.0264101 | 1 | 5 | amine transport |
| 99 | GO:0045039 | 0.0261423 | 48.787037 | 0.0264101 | 1 | 5 | protein import into mitochondrial inner membrane |
| 100 | GO:0016049 | 0.0303228 | 8.035385 | 0.2746652 | 2 | 52 | cell growth |
| 101 | GO:2001056 | 0.0312911 | 39.022222 | 0.0316921 | 1 | 6 | positive regulation of cysteine-type endopeptidase activity |
| 102 | GO:0046323 | 0.0312911 | 39.022222 | 0.0316921 | 1 | 6 | glucose import |
| 103 | GO:0046324 | 0.0312911 | 39.022222 | 0.0316921 | 1 | 6 | regulation of glucose import |
| 104 | GO:0070570 | 0.0312911 | 39.022222 | 0.0316921 | 1 | 6 | regulation of neuron projection regeneration |
| 105 | GO:0014013 | 0.0312911 | 39.022222 | 0.0316921 | 1 | 6 | regulation of gliogenesis |
| 106 | GO:0015844 | 0.0312911 | 39.022222 | 0.0316921 | 1 | 6 | monoamine transport |
| 107 | GO:0030879 | 0.0312911 | 39.022222 | 0.0316921 | 1 | 6 | mammary gland development |
| 108 | GO:0005975 | 0.0345276 | 4.602090 | 0.7236370 | 3 | 137 | carbohydrate metabolic process |
| 109 | GO:0009152 | 0.0359127 | 7.297902 | 0.3010753 | 2 | 57 | purine ribonucleotide biosynthetic process |
| 110 | GO:0050771 | 0.0364137 | 32.512346 | 0.0369742 | 1 | 7 | negative regulation of axonogenesis |
| 111 | GO:0050679 | 0.0364137 | 32.512346 | 0.0369742 | 1 | 7 | positive regulation of epithelial cell proliferation |
| 112 | GO:0060688 | 0.0364137 | 32.512346 | 0.0369742 | 1 | 7 | regulation of morphogenesis of a branching structure |
| 113 | GO:0031102 | 0.0364137 | 32.512346 | 0.0369742 | 1 | 7 | neuron projection regeneration |
| 114 | GO:0010950 | 0.0364137 | 32.512346 | 0.0369742 | 1 | 7 | positive regulation of endopeptidase activity |
| 115 | GO:0031644 | 0.0364137 | 32.512346 | 0.0369742 | 1 | 7 | regulation of neurological system process |
| 116 | GO:0019233 | 0.0364137 | 32.512346 | 0.0369742 | 1 | 7 | sensory perception of pain |
| 117 | GO:0046390 | 0.0382529 | 7.039136 | 0.3116393 | 2 | 59 | ribose phosphate biosynthetic process |
| 118 | GO:0009260 | 0.0382529 | 7.039136 | 0.3116393 | 2 | 59 | ribonucleotide biosynthetic process |
| 119 | GO:0006164 | 0.0394446 | 6.916446 | 0.3169213 | 2 | 60 | purine nucleotide biosynthetic process |
| 120 | GO:0006839 | 0.0394446 | 6.916446 | 0.3169213 | 2 | 60 | mitochondrial transport |
| 121 | GO:0048709 | 0.0415101 | 27.862434 | 0.0422562 | 1 | 8 | oligodendrocyte differentiation |
| 122 | GO:1904659 | 0.0415101 | 27.862434 | 0.0422562 | 1 | 8 | glucose transmembrane transport |
| 123 | GO:0001837 | 0.0415101 | 27.862434 | 0.0422562 | 1 | 8 | epithelial to mesenchymal transition |
| 124 | GO:0010827 | 0.0415101 | 27.862434 | 0.0422562 | 1 | 8 | regulation of glucose transmembrane transport |
| 125 | GO:0090151 | 0.0415101 | 27.862434 | 0.0422562 | 1 | 8 | establishment of protein localization to mitochondrial membrane |
| 126 | GO:0010952 | 0.0415101 | 27.862434 | 0.0422562 | 1 | 8 | positive regulation of peptidase activity |
| 127 | GO:0030516 | 0.0415101 | 27.862434 | 0.0422562 | 1 | 8 | regulation of axon extension |
| 128 | GO:0009117 | 0.0419590 | 4.243862 | 0.7817393 | 3 | 148 | nucleotide metabolic process |
| 129 | GO:0072522 | 0.0431041 | 6.572509 | 0.3327674 | 2 | 63 | purine-containing compound biosynthetic process |
| 130 | GO:0006753 | 0.0441167 | 4.155405 | 0.7975854 | 3 | 151 | nucleoside phosphate metabolic process |
| 131 | GO:0032526 | 0.0465805 | 24.375000 | 0.0475382 | 1 | 9 | response to retinoic acid |
| 132 | GO:0007007 | 0.0465805 | 24.375000 | 0.0475382 | 1 | 9 | inner mitochondrial membrane organization |
| 133 | GO:0015749 | 0.0465805 | 24.375000 | 0.0475382 | 1 | 9 | monosaccharide transmembrane transport |
| 134 | GO:0010977 | 0.0465805 | 24.375000 | 0.0475382 | 1 | 9 | negative regulation of neuron projection development |
| 135 | GO:0035458 | 0.0465805 | 24.375000 | 0.0475382 | 1 | 9 | cellular response to interferon-beta |
| 136 | GO:0008645 | 0.0465805 | 24.375000 | 0.0475382 | 1 | 9 | hexose transmembrane transport |
Module 14
GO_term_cyan <- read.csv("/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/GO_term_cyan.csv")
GO_term_cyan %>%
kbl() %>%
kable_styling(bootstrap_options = "striped", full_width = F, position = "left") %>%
kable_paper() %>%
scroll_box(width = "800px", height = "200px")| X | GOBPID | Pvalue | OddsRatio | ExpCount | Count | Size | Term |
|---|---|---|---|---|---|---|---|
| 1 | GO:0030838 | 0.0000109 | 102.642857 | 0.0471609 | 3 | 25 | positive regulation of actin filament polymerization |
| 2 | GO:0030833 | 0.0000281 | 72.718894 | 0.0641388 | 3 | 34 | regulation of actin filament polymerization |
| 3 | GO:0030041 | 0.0000307 | 70.433036 | 0.0660253 | 3 | 35 | actin filament polymerization |
| 4 | GO:0008064 | 0.0000334 | 68.285714 | 0.0679117 | 3 | 36 | regulation of actin polymerization or depolymerization |
| 5 | GO:0030832 | 0.0000334 | 68.285714 | 0.0679117 | 3 | 36 | regulation of actin filament length |
| 6 | GO:0032273 | 0.0000426 | 62.559524 | 0.0735710 | 3 | 39 | positive regulation of protein polymerization |
| 7 | GO:0008154 | 0.0000461 | 60.857143 | 0.0754575 | 3 | 40 | actin polymerization or depolymerization |
| 8 | GO:0110053 | 0.0000534 | 57.714286 | 0.0792303 | 3 | 42 | regulation of actin filament organization |
| 9 | GO:0031334 | 0.0000615 | 54.878049 | 0.0830032 | 3 | 44 | positive regulation of protein complex assembly |
| 10 | GO:1902905 | 0.0000658 | 53.561225 | 0.0848896 | 3 | 45 | positive regulation of supramolecular fiber organization |
| 11 | GO:0051495 | 0.0000800 | 49.961905 | 0.0905490 | 3 | 48 | positive regulation of cytoskeleton organization |
| 12 | GO:0032271 | 0.0000800 | 49.961905 | 0.0905490 | 3 | 48 | regulation of protein polymerization |
| 13 | GO:0032956 | 0.0000851 | 48.866460 | 0.0924354 | 3 | 49 | regulation of actin cytoskeleton organization |
| 14 | GO:0051127 | 0.0001145 | 188.714286 | 0.0169779 | 2 | 9 | positive regulation of actin nucleation |
| 15 | GO:0032535 | 0.0001205 | 43.178571 | 0.1037540 | 3 | 55 | regulation of cellular component size |
| 16 | GO:0043254 | 0.0001341 | 41.563492 | 0.1075269 | 3 | 57 | regulation of protein complex assembly |
| 17 | GO:0051125 | 0.0001430 | 165.093750 | 0.0188644 | 2 | 10 | regulation of actin nucleation |
| 18 | GO:0051258 | 0.0001564 | 39.353383 | 0.1131862 | 3 | 60 | protein polymerization |
| 19 | GO:0032970 | 0.0001643 | 38.667488 | 0.1150726 | 3 | 61 | regulation of actin filament-based process |
| 20 | GO:1902903 | 0.0001809 | 37.364286 | 0.1188455 | 3 | 63 | regulation of supramolecular fiber organization |
| 21 | GO:0007015 | 0.0001896 | 36.744731 | 0.1207319 | 3 | 64 | actin filament organization |
| 22 | GO:0090066 | 0.0002079 | 35.564626 | 0.1245048 | 3 | 66 | regulation of anatomical structure size |
| 23 | GO:0051493 | 0.0002477 | 33.415778 | 0.1320506 | 3 | 70 | regulation of cytoskeleton organization |
| 24 | GO:0044089 | 0.0003287 | 30.214286 | 0.1452556 | 3 | 77 | positive regulation of cellular component biogenesis |
| 25 | GO:0042752 | 0.0005977 | 73.236111 | 0.0377287 | 2 | 20 | regulation of circadian rhythm |
| 26 | GO:0010638 | 0.0006494 | 23.694529 | 0.1829843 | 3 | 97 | positive regulation of organelle organization |
| 27 | GO:0045010 | 0.0007252 | 65.887500 | 0.0415016 | 2 | 22 | actin nucleation |
| 28 | GO:0097435 | 0.0011797 | 19.119458 | 0.2244859 | 3 | 119 | supramolecular fiber organization |
| 29 | GO:0044087 | 0.0014249 | 17.858295 | 0.2395774 | 3 | 127 | regulation of cellular component biogenesis |
| 30 | GO:0030036 | 0.0014576 | 17.712000 | 0.2414639 | 3 | 128 | actin cytoskeleton organization |
| 31 | GO:0030029 | 0.0014908 | 17.568027 | 0.2433503 | 3 | 129 | actin filament-based process |
| 32 | GO:0007623 | 0.0015416 | 43.841667 | 0.0603660 | 2 | 32 | circadian rhythm |
| 33 | GO:0051130 | 0.0023917 | 14.790029 | 0.2867384 | 3 | 152 | positive regulation of cellular component organization |
| 34 | GO:0033043 | 0.0032381 | 13.231497 | 0.3188078 | 3 | 169 | regulation of organelle organization |
| 35 | GO:0048511 | 0.0037389 | 27.307292 | 0.0943218 | 2 | 50 | rhythmic process |
| 36 | GO:0034622 | 0.0045142 | 11.697479 | 0.3584229 | 3 | 190 | cellular protein-containing complex assembly |
| 37 | GO:0007010 | 0.0057460 | 10.686975 | 0.3904924 | 3 | 207 | cytoskeleton organization |
| 38 | GO:0065003 | 0.0082843 | 9.303495 | 0.4451990 | 3 | 236 | protein-containing complex assembly |
| 39 | GO:0043933 | 0.0120052 | 8.064205 | 0.5093379 | 3 | 270 | protein-containing complex subunit organization |
| 40 | GO:0051128 | 0.0137819 | 7.641078 | 0.5357480 | 3 | 284 | regulation of cellular component organization |
| 41 | GO:0045892 | 0.0232698 | 10.165354 | 0.2433503 | 2 | 129 | negative regulation of transcription, DNA-templated |
| 42 | GO:1902679 | 0.0239515 | 10.003876 | 0.2471232 | 2 | 131 | negative regulation of RNA biosynthetic process |
| 43 | GO:1903507 | 0.0239515 | 10.003876 | 0.2471232 | 2 | 131 | negative regulation of nucleic acid-templated transcription |
| 44 | GO:0051253 | 0.0242955 | 9.925000 | 0.2490096 | 2 | 132 | negative regulation of RNA metabolic process |
| 45 | GO:2000113 | 0.0271218 | 9.335145 | 0.2641011 | 2 | 140 | negative regulation of cellular macromolecule biosynthetic process |
| 46 | GO:0045934 | 0.0278489 | 9.198214 | 0.2678740 | 2 | 142 | negative regulation of nucleobase-containing compound metabolic process |
| 47 | GO:0010558 | 0.0285840 | 9.065141 | 0.2716469 | 2 | 144 | negative regulation of macromolecule biosynthetic process |
| 48 | GO:0006508 | 0.0298147 | 5.602204 | 0.7149594 | 3 | 379 | proteolysis |
| 49 | GO:0031327 | 0.0300782 | 8.809931 | 0.2791926 | 2 | 148 | negative regulation of cellular biosynthetic process |
| 50 | GO:0009890 | 0.0312196 | 8.627517 | 0.2848519 | 2 | 151 | negative regulation of biosynthetic process |
| 51 | GO:0022607 | 0.0345436 | 5.268844 | 0.7564610 | 3 | 401 | cellular component assembly |
| 52 | GO:0065008 | 0.0389387 | 5.009250 | 0.7923033 | 3 | 420 | regulation of biological quality |
Figure 2c. Correlating virus interaction and virus-varroa interactions
To test if we can predict the virus-varroa interaction given the virus abundance, we used Mantel-test for correlation between two distance-matrices (Mantel 1967).
# load the two matrices:
# the module–trait association matrix:
load(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/moduleTraitCor_66.RData")
# and the viral abundance correlogram:
virusAbundCor_66 <- readRDS(file = "/Users/nuriteliash/Documents/GitHub/varroa-virus-networks/results/virusAbundCor_66.rds")
virusAbundCor_66 <- virusAbundCor_66$corr
# make correlation matrix of the "moduleTraitCor":
corModulTrait_66 <- cor(moduleTraitCor_66)
# (1) Mantel test using "ape" library:
mantel.test(corModulTrait_66, virusAbundCor_66, graph = TRUE,
main = "Mantel test",
xlab = "z-statistic", ylab = "Density",
sub = "The vertical line shows the observed z-statistic")
## $z.stat
## [1] 6.276091
##
## $p
## [1] 0.001
##
## $alternative
## [1] "two.sided"# (2) Mantel test using "vegan" library:
mantel(corModulTrait_66, virusAbundCor_66, method="pearson", permutations=1000)##
## Mantel statistic based on Pearson's product-moment correlation
##
## Call:
## mantel(xdis = corModulTrait_66, ydis = virusAbundCor_66, method = "pearson", permutations = 1000)
##
## Mantel statistic r: 0.6044
## Significance: 0.000999
##
## Upper quantiles of permutations (null model):
## 90% 95% 97.5% 99%
## 0.129 0.170 0.200 0.243
## Permutation: free
## Number of permutations: 1000#plot the correlation
#sizeGrWindow(9, 5)
verboseScatterplot(x = corModulTrait_66, y = virusAbundCor_66, main = "Correlation between Fig 2a, \n virus-virus interaction; and Fig 2b, \n varroa-virus interaction", xlab = "Correlation of viral interaction \nwith varroa modules", ylab = "Correlation of viral abundance", abline = T, abline.color = "black", bg = "black", cex.lab = 1.2, cex.main = 1, cex.axis = 1)
Figure 2c. Intra-viral interactions can predict virus - vector interactions. Correlation model between viral load correlations (fig 2a), and the distance-matrix of the module-virus correlations (fig 2b). For analysis in figure c, Mantel test for correlation between two matrices was conducted using 1,000 permutations.
In figure 2c, X-axis: how virus interacts with varroa expression, and Y-axis: the correlation of viral abundance across samples.
We found a significant positive correlation between the two distance matrices (Mantel-test for correlation between two distance-matrices (Mantel 1967), Mantel statistic r = 0.604, p = 0.001) (Fig 2c). Meaning, given viruses’ interaction we can predict how these viruses will interact with the vector’s module.